From bdd2cc2c57f05111606efbfbef809fb88b883601 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jan 2024 11:58:32 +0100 Subject: [PATCH 001/524] adding easyconfigs: GROMACS-2023.4-foss-2023a.eb --- .../g/GROMACS/GROMACS-2023.4-foss-2023a.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb new file mode 100644 index 00000000000..2eecebb2ae3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb @@ -0,0 +1,86 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.4.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 47ce27b1fd766bf2665955ae6fc4aa4eca5ade99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jan 2024 12:00:29 +0100 Subject: [PATCH 002/524] split long line --- easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb index 2eecebb2ae3..e8c0d929bd9 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb @@ -72,7 +72,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.2', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.4.tar.gz', 'start_dir': 'python_packaging/gmxapi', 'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'], From 03b4db7bf7e3ee1aecf374f15bb39981419be358 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Mar 2024 11:43:32 +0100 Subject: [PATCH 003/524] strip Suprressor out of ResistanceGA --- .../Circuitscape-5.12.3-Julia-1.9.2.eb | 4 +++- ...-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 12 +++------- ...GA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 17 ++------------ .../Suppressor-0.2.4-Julia-1.9.2.eb | 22 +++++++++++++++++++ 4 files changed, 30 insertions(+), 25 deletions(-) create mode 100644 easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index a6649359df9..f9909fe5c7a 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -403,6 +403,8 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index a7789bd8358..4da1b0f58aa 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -16,8 +16,6 @@ dependencies = [ ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), ] -preinstallopts = "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && " - exts_default_options = { 'source_tmpl': 'v%(version)s.tar.gz', } @@ -224,17 +222,13 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"%(name)s\")'"] +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", +] sanity_check_paths = { 'files': [], 'dirs': ['packages/%(name)s'], } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 83987de1e5a..cd1ffb55617 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -14,8 +14,9 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), + ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), - ('RCall', '0.13.17', versionsuffix), + ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM), ] exts_defaultclass = 'RPackage' @@ -31,14 +32,6 @@ exts_default_options = { } exts_list = [ - ('Suppressor', '0.2.4', { - 'easyblock': 'JuliaPackage', - 'exts_filter': ("julia -e 'using %(ext_name)s'", ''), - 'preinstallopts': "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && ", - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'], - 'checksums': ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'], - }), ('GA', '3.2.2', { 'checksums': ['6245c634a11b8414bde7ed326b8c615512645489b19969619484c865e900bf8c'], }), @@ -73,12 +66,6 @@ modextrapaths = { 'R_LIBS_SITE': '', } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - sanity_check_paths = { 'files': [], 'dirs': ['%(name)s'], diff --git a/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb new file mode 100644 index 00000000000..5b443b3fac5 --- /dev/null +++ b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'JuliaPackage' + +name = 'Suppressor' +version = '0.2.4' +_julia_ver = '1.9.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaIO/Suppressor.jl' +description = """Julia macros for suppressing and/or capturing output (STDOUT), +warnings (STDERR) or both streams at the same time.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/JuliaIO/Suppressor.jl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'] + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +moduleclass = 'lib' From 210f57ecfaf72ab3ad6416849c96b721247acbde Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Mar 2024 17:02:40 +0100 Subject: [PATCH 004/524] fix codestyle in ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb --- .../ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index cd1ffb55617..03e40a493f2 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), - ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) + ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM), ] From ac616dc76259925429a595e1a52bd5657cb79089 Mon Sep 17 00:00:00 2001 From: satishk Date: Wed, 27 Mar 2024 16:43:24 +0100 Subject: [PATCH 005/524] adding easyconfigs: Paraver-4.11.4-foss-2023a.eb --- .../p/Paraver/Paraver-4.11.4-foss-2023a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb new file mode 100644 index 00000000000..e92b712357a --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.11.4' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['8f65fbeacaef003b544ecc0244a4ed9a99e9521cdd027889106fbce0b052fd8d'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('wxWidgets', '3.2.2.1'), +] + +moduleclass = 'perf' From 92d11fb4e3897a44a2e8e6f50eb4770f0630a9b6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 12 Apr 2024 13:52:59 +0200 Subject: [PATCH 006/524] adding easyconfigs: Gradio-4.19.0-foss-2023a.eb --- .../g/Gradio/Gradio-4.19.0-foss-2023a.eb | 123 ++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb new file mode 100644 index 00000000000..4c3556a27cd --- /dev/null +++ b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb @@ -0,0 +1,123 @@ +easyblock = 'PythonBundle' + +name = 'Gradio' +version = '4.19.0' + +homepage = "https://www.gradio.app" +description = """ +Gradio is an open-source Python package that allows you to quickly build a demo or web +application for your machine learning model, API, or any arbitrary Python function. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('pydantic', '2.5.3'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), + ('tqdm', '4.66.1'), + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hatch-requirements-txt', '0.4.1', { + 'source_tmpl': 'hatch_requirements_txt-%(version)s.tar.gz', + 'checksums': ['2c686e5758fd05bb55fa7d0c198fdd481f8d3aaa3c693260f5c0d74ce3547d20'], + }), + ('aiofiles', '23.2.1', { + 'checksums': ['84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('starlette', '0.36.3', { + 'checksums': ['90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080'], + }), + ('typing-extensions', '4.8.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('fastapi', '0.109.2', { + 'checksums': ['f3817eac96fe4f65a2ebb4baa000f394e55f5fccdaf7f75250804bc58f354f73'], + }), + ('ffmpy', '0.3.2', { + 'checksums': ['475ebfff1044661b8d969349dbcd2db9bf56d3ee78c0627e324769b49a27a78f'], + }), + ('websockets', '11.0.3', { + 'checksums': ['88fc51d9a26b10fc331be344f1781224a375b78488fc343620184e95a4b27016'], + }), + ('gradio-client', '0.10.0', { + 'source_tmpl': 'gradio_client-%(version)s.tar.gz', + 'checksums': ['feaee70f18363d76f81a7d25fc3456f40ed5f92417e642c8f1bf86dc65e3a981'], + }), + ('huggingface-hub', '0.20.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['94e7f8e074475fbc67d6a71957b678e1b4a74ff1b64a644fd6cbb83da962d05d'], + }), + ('orjson', '3.9.14', { + 'checksums': ['06fb40f8e49088ecaa02f1162581d39e2cf3fd9dbbfe411eb2284147c99bad79'], + }), + ('pydub', '0.25.1', { + 'checksums': ['980a33ce9949cab2a569606b65674d748ecbca4f0796887fd6f46173a7b0d30f'], + }), + ('python-multipart', '0.0.9', { + 'modulename': 'multipart', + 'source_tmpl': 'python_multipart-%(version)s.tar.gz', + 'checksums': ['03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026'], + }), + ('ruff', '0.2.1', { + 'checksums': ['3b42b5d8677cd0c72b99fcaf068ffc62abb5a19e71b4a3b9cfa50658a0af02f1'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.27.1', { + 'checksums': ['3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a'], + }), + ('anyio', '4.2.0', { + 'checksums': ['e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f'], + }), + ('httpcore', '1.0.3', { + 'checksums': ['5c0f9546ad17dac4d0772b0808856eb616eb8b48ce94f49ed819fd6982a8a544'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('httpx', '0.26.0', { + 'checksums': ['451b55c30d5185ea6b23c2c793abf9bb237d2a7dfb901ced6ff69ad37ec1dfaf'], + }), + ('importlib-resources', '6.1.1', { + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a'], + }), + ('Jinja2', '3.1.3', { + 'checksums': ['ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90'], + }), + ('tomlkit', '0.12.0', { + 'checksums': ['01f0477981119c7d8ee0f67ebe0297a7c95b14cf9f4b102b45486deb77018716'], + }), + ('gradio', version, { + 'checksums': ['e77e3ce8a4113865abd1dcf92cc9426d9da4896e0a6fd2824a0c90ec751dd442'], + }), +] + +moduleclass = 'ai' From 82af54e32a595093f8fc4517b2c550e7c2d72a0e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jun 2024 11:18:41 +0100 Subject: [PATCH 007/524] adding easyconfigs: arrow-R-16.1.0-foss-2023b-R-4.4.1.eb, R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb --- .../arrow-R-16.1.0-foss-2023b-R-4.4.1.eb | 37 + ...le-Bioconductor-3.19-foss-2023b-R-4.4.1.eb | 1365 +++++++++++++++++ 2 files changed, 1402 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb new file mode 100644 index 00000000000..c6aa492f2db --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb @@ -0,0 +1,37 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '16.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://archive.apache.org/dist/arrow/arrow-%(version)s', # full Arrow source tarballs +] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'] + +dependencies = [ + ('R', '4.4.1'), + ('R-bundle-CRAN', '2024.06'), + ('Arrow', '16.1.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z +] + +start_dir = 'r' +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb new file mode 100644 index 00000000000..6e3261a44b0 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb @@ -0,0 +1,1365 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.19' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('pkgconf', '2.0.3')] + +dependencies = [ + ('R', '4.4.1'), + ('Boost', '1.83.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('arrow-R', '16.1.0', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.19/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'sources': ['%(name)s_%(version)s.tar.gz'], +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('BiocGenerics', '0.50.0', { 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['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], + }), + ('RnBeads', '2.22.0', { + 'checksums': ['720b927f27713b7a16d703a1c77c1cb481f2c263b625a064dd004fed57fded6c'], + }), + ('RnBeads.hg19', '1.36.0', { + 'checksums': ['c991085a2420b01c075b1f3a27645ed4c7a3b8e11b5c9efa52e6c4b4ffb0c77a'], + }), + ('RnBeads.hg38', '1.36.0', { + 'checksums': ['1498b7131f3e30fc3860977829f8c457306bdd364e3a8807b5367d7314eace15'], + }), + ('RnBeads.mm9', '1.36.0', { + 'checksums': ['0b9456e3c19d7f9cd62a36290bc6d048d5eeae2fa09fbe701d2d4c59a292a5ad'], + }), + ('RnBeads.mm10', '2.12.0', { + 'checksums': ['d4b5f53c0b5da080f7c252965032e250a657e41a80c8181c28c8b9327cdd3194'], + }), + ('RnBeads.rn5', '1.36.0', { + 'checksums': ['8e384bffbe6de580c00779415fd7fefb7f01a7b9e0090a11200f284680f11b25'], + }), + ('log4r', '0.4.3', { + 'checksums': ['dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c'], + }), + ('MSstatsConvert', '1.14.0', { + 'checksums': ['f55f9381d611b80027c489e52de539d8261d84671817b82afeaa617266e45de0'], + }), + ('MSstats', '4.12.0', { + 'checksums': ['773bfef999416c0c0f5f207984991e9cf209598cd6ae32411aae76bd2404305b'], + }), + ('MSstatsTMT', '2.12.1', { + 'checksums': ['f676d71dcd9abfe2eb88b909dc9945622ed19e50bd482f486a7ce4850be4d60e'], + }), + ('MSstatsPTM', '2.6.0', { + 'checksums': ['7063d7c540b188cbf20c083c94d28431e2ecd8fc47c7630d8c5c67ae44eb6c47'], + }), + ('factoextra', '1.0.7', { + 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], + }), + ('MSstatsLiP', '1.10.0', { + 'checksums': ['40a60aef2d736da2936f1a4b624a962ed69490e6e38a2587df8b6cf5eff2eece'], + }), + ('babelgene', '22.9', { + 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + ('escape', '2.0.0', { + 'checksums': ['5dfcdaf7d1b1836c276a1284ebbc6bbcaeb35da11805a2491bd4cb795acf8b0f'], + }), + ('plyranges', '1.24.0', { + 'checksums': ['a8505d774d0cf9c1488205343abd1817dd5d016082597bb173d002d496a10566'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 40baa44bcae46d9f3e9932d2962d444aaad076f8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jun 2024 11:44:13 +0100 Subject: [PATCH 008/524] use CRAN source for arrow-R --- .../a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb index c6aa492f2db..dd2e4260145 100644 --- a/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb @@ -13,10 +13,9 @@ source_urls = [ 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - 'https://archive.apache.org/dist/arrow/arrow-%(version)s', # full Arrow source tarballs ] -sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['66c1586ee7becd65b4d21b11ffcd157dc19f75c3c10ff5c5b3610689aadce7ef'] dependencies = [ ('R', '4.4.1'), @@ -24,7 +23,6 @@ dependencies = [ ('Arrow', '16.1.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z ] -start_dir = 'r' preinstallopts = "export LIBARROW_BINARY=true && " sanity_check_paths = { From c2e30f8bb49e38370ac6c72350bb9292b370c1fc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 9 Jul 2024 16:30:19 +0200 Subject: [PATCH 009/524] adding easyconfigs: xESMF-0.8.6-foss-2023a.eb --- .../x/xESMF/xESMF-0.8.6-foss-2023a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb new file mode 100644 index 00000000000..56456f83e30 --- /dev/null +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'xESMF' +version = '0.8.6' + +homepage = 'https://xesmf.readthedocs.io' +description = "xESMF: Universal Regridder for Geospatial Data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ESMPy', '8.6.0'), + ('numba', '0.58.1'), + ('Shapely', '2.0.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True + +exts_list = [ + ('cf_xarray', '0.9.3', { + 'checksums': ['5012444078964ef931cdc71d559f58488edd5fa9a175fbec326f9356e481b2cf'], + }), + ('sparse', '0.14.0', { + 'checksums': ['5f5827a37f6cd6f6730a541f994c95c60a3ae2329e01f4ba21ced5339aea0098'], + }), + ('xesmf', version, { + 'checksums': ['61c54f0db19fe4871623791db50b1ae589ea1a834d0df461cb58ffbd10d875de'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 3cfe7df8efbcdc5518067144db7088dd899793b3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Jul 2024 15:35:54 +0200 Subject: [PATCH 010/524] run tests of xESMF v0.8.6 --- .../easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb index 56456f83e30..c77c2e324ed 100644 --- a/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb @@ -8,6 +8,10 @@ description = "xESMF: Universal Regridder for Geospatial Data" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pytest', '7.4.2'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -15,11 +19,15 @@ dependencies = [ ('numba', '0.58.1'), ('Shapely', '2.0.1'), ('xarray', '2023.9.0'), + ('dask', '2023.9.2'), ] use_pip = True exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), ('cf_xarray', '0.9.3', { 'checksums': ['5012444078964ef931cdc71d559f58488edd5fa9a175fbec326f9356e481b2cf'], }), @@ -28,6 +36,9 @@ exts_list = [ }), ('xesmf', version, { 'checksums': ['61c54f0db19fe4871623791db50b1ae589ea1a834d0df461cb58ffbd10d875de'], + 'runtest': 'pytest', + 'testopts': "-v --pyargs xesmf", + 'testinstall': True, }), ] From 8a12c59b37315a2adae17bce4264a893237f59d2 Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Thu, 25 Jul 2024 14:46:03 +0100 Subject: [PATCH 011/524] adding easyconfigs: OpenMM-8.1.2-foss-2023b.eb --- .../o/OpenMM/OpenMM-8.1.2-foss-2023b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb new file mode 100644 index 00000000000..7b4e30add53 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.1.2' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['afc888a4e46486d8d68dac4d403e2b0b28f51b95e52e821e34c38e8b428e040e'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('SWIG', '4.1.1'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 65f1a2586dadb4b7e40e34ca6689838ca22c7ddc Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Mon, 29 Jul 2024 11:16:02 +0100 Subject: [PATCH 012/524] adding easyconfigs: ASE-3.23.0-gfbf-2023b.eb --- .../a/ASE/ASE-3.23.0-gfbf-2023b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb new file mode 100644 index 00000000000..07ad1ecc555 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('Flask', '3.0.0'), + ('matplotlib', '3.8.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From d55ea57137f846e1197c501b208d24aaaa2589d0 Mon Sep 17 00:00:00 2001 From: software Date: Thu, 15 Aug 2024 14:56:04 +0000 Subject: [PATCH 013/524] adding easyconfigs: BGEN-enkre-1.1.7-GCC-12.3.0.eb, Boost-1.55.0-GCC-12.3.0.eb --- .../BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb | 73 +++++++++++++++++++ .../b/Boost/Boost-1.55.0-GCC-12.3.0.eb | 21 ++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..bf5a35b052b --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb @@ -0,0 +1,73 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('SQLite', '3.42.0'), + ('zstd', '1.5.5'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..e7cdaf16fbd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' From 8cd363914ace2cb429f5057584dd987aa3b49460 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 10:22:39 +0200 Subject: [PATCH 014/524] Add files via upload --- .../AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb | 163 ++++++++++++ .../AlphaFold-2.3.2_BioPythonSCOPData.patch | 14 + ...a-dep-paths-shebang-UniRef30_2023_02.patch | 175 +++++++++++++ .../AlphaFold-2.3.2_use_openmm_8.0.0.patch | 243 ++++++++++++++++++ 4 files changed, 595 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..44e43d11b86 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,163 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1') +] + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.13.0'), # doesn't require TF-gpu + ('Biopython', '1.83'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.4'), + ('Kalign', '3.4.0'), + ('jax', '0.4.25', versionsuffix), # also provides absl-py # requirement is ==0.3.25! + ('UCX-CUDA', '1.14.1', versionsuffix), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('OpenMM', '8.0.0', versionsuffix), + ('dm-tree', '0.1.8'), + ('dm-haiku', '0.0.11', versionsuffix), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + ('stereo_chemical_props.txt', local_scp_commit, { + 'easyblock': 'Binary', + 'source_urls': [ + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s ./stereo_chemical_props.txt", + } + ], + 'checksums': [ + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + ] + }) +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '7.0.0', { + 'checksums': ['323736fb92cd9418fc5e7133bc953e11a9da04f4483f828b527db553f1e7e5a3'], + }), + ('immutabledict', '4.1.0', { + 'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + (name, version, { + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.2_use_openmm_8.0.0.patch', + 'AlphaFold-2.3.2_BioPythonSCOPData.patch', + ], + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': [ + {'AlphaFold-2.3.2.tar.gz': '4ea8005ba1b573fa1585e4c29b7d188c5cbfa59b4e4761c9f0c15c9db9584a8e'}, + {'AlphaFold-2.0.0_fix-packages.patch': '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db'}, + {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch': + '72a7b7cb8be4105f7bd32b404454afa465300d16b1ccc9933c9a70873f134f4e'}, + {'AlphaFold-2.0.0_n-cpu.patch': 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04'}, + {'AlphaFold-2.0.1_setup_rm_tfcpu.patch': + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'}, + {'AlphaFold-2.3.2_use_openmm_8.0.0.patch': + 'bbef940c0c959040aaf3984ec47777a229c164517b54616a2688d58fae636d84'}, + {'AlphaFold-2.3.2_BioPythonSCOPData.patch': + '5aedd5a35da6d0a993ca19f4de807cf77ec36a5a52c97100110a0c5475cef1b8'}, + ], + }), +] + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +local_link_scp = 'ln -s %%(installdir)s/stereo_chemical_props.txt %s/alphafold/common' % local_pylibdir + +postinstallcmds = [ + 'cp %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold*.py %(installdir)s/bin', + 'cp -rpP %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s', + 'cd %(installdir)s/bin && ln -s run_alphafold.py alphafold', + 'chmod a+x %(installdir)s/bin/run_alphafold.py', + local_link_scp, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "python %(installdir)s/bin/run_alphafold_test.py", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; + # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py + 'TF_FORCE_UNIFIED_MEMORY': '1', + # jaxlib 0.4.1: https://jax.readthedocs.io/en/latest/changelog.html#jaxlib-0-4-1-dec-13-2022 + # "The behavior of XLA_PYTHON_CLIENT_MEM_FRACTION=.XX has been changed to allocate XX% of the total GPU memory + # instead of the previous behavior of using currently available GPU memory to calculate preallocation. Please refer + # to GPU memory allocation for more details." + # https://jax.readthedocs.io/en/latest/gpu_memory_allocation.html + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '2.5', + # + # Download with $EBROOTALPHAFOLD/scripts/download_all_data.sh /path/to/AlphaFold_DBs/$EBVERSIONALPHAFOLD + 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs/%(versions)s', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +modloadmsg = """Unlike previous modules, this module is using the updated UniRef30_2023_02 by default! +In order to use the old UniRef30, please explicitly pass the command line parameter: +--uniref30_database_path $ALPHAFOLD_DATA_DIR/uniref30/UniRef30_2021_03""" + +# Remark: Please modify $EBROOTALPHAFOLD/scripts/download_uniref30.sh in order to download old UniRef30 2021.03 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch new file mode 100644 index 00000000000..893b7f0483f --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch @@ -0,0 +1,14 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +# BioPython 1.83 does not provide protein_letters_3to1 in Bio.Data.SCOPdata but in Bio.Data.IUPACData +diff -ru -ru alphafold-2.3.2/alphafold/data/mmcif_parsing.py alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py +--- alphafold-2.3.2/alphafold/data/mmcif_parsing.py 2024-02-19 09:55:16.359778490 +0100 ++++ alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py 2023-03-27 13:50:49.000000000 +0200 +@@ -21,7 +21,7 @@ + + from absl import logging + from Bio import PDB +-from Bio.Data import SCOPData ++from Bio.Data import IUPACData as SCOPData + + # Type aliases: + ChainId = str diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch new file mode 100644 index 00000000000..c84bb7710d6 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch @@ -0,0 +1,175 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0/2.1.2/2.3.0/2.3.2: Thomas Hoffmann (EMBL); +update to uniref30 2023.02 (THEMBL) + +diff -ru alphafold-2.3.2/run_alphafold.py alphafold-2.3.2_data-dep-paths/run_alphafold.py +--- alphafold-2.3.2/run_alphafold.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_data-dep-paths/run_alphafold.py 2023-04-06 09:59:41.304466108 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + # Copyright 2021 DeepMind Technologies Limited + # + # Licensed under the Apache License, Version 2.0 (the "License"); +@@ -42,6 +43,46 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2023_02') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -59,7 +100,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -71,32 +112,32 @@ + flags.DEFINE_string('hmmsearch_binary_path', shutil.which('hmmsearch'), + 'Path to the hmmsearch executable.') + flags.DEFINE_string('hmmbuild_binary_path', shutil.which('hmmbuild'), +- 'Path to the hmmbuild executable.') ++ 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), +- 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' +- 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' +- 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' +- 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' +- 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' +- 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' +- 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' +- 'template mmCIF structures, each named .cif') ++ 'Path to the Kalign executable.') ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' ++ 'version of BFD used with the "reduced_dbs" preset.') ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' ++ 'database for use by JackHMMer.') ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' ++ 'database for use by HHsearch.') ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' ++ 'seqres database for use by hmmsearch.') ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' ++ 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' +- 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' +- 'mapping from obsolete PDB IDs to the PDB IDs of their ' +- 'replacements.') ++ 'to consider. Important if folding historical test sets.') ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' ++ 'mapping from obsolete PDB IDs to the PDB IDs of their ' ++ 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', + ['full_dbs', 'reduced_dbs'], + 'Choose preset MSA database configuration - ' +@@ -137,7 +178,7 @@ + 'distracting stereochemical violations but might help ' + 'in case you are having issues with the relaxation ' + 'stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -334,6 +375,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -456,13 +501,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) +diff -ru alphafold-2.3.2/scripts/download_uniref30.sh alphafold-2.3.2_uniref30/scripts/download_uniref30.sh +--- alphafold-2.3.2/scripts/download_uniref30.sh 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_uniref30/scripts/download_uniref30.sh 2024-02-19 14:41:57.295409862 +0100 +@@ -33,7 +33,8 @@ + ROOT_DIR="${DOWNLOAD_DIR}/uniref30" + # Mirror of: + # https://wwwuser.gwdg.de/~compbiol/uniclust/2021_03/UniRef30_2021_03.tar.gz +-SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz" ++#SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz" ++SOURCE_URL="https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz" + BASENAME=$(basename "${SOURCE_URL}") + + mkdir --parents "${ROOT_DIR}" diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch new file mode 100644 index 00000000000..765fdb3c4d6 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch @@ -0,0 +1,243 @@ +# Add compatibility with OpenMM-8.0.0 +# The patch is based on the recipe from https://github.com/deepmind/alphafold/issues/404 +# Author: maxim-masterov (SURF) (7.7.0) +# update 8.0.0: THEMBL +diff -ru alphafold-2.3.2/alphafold/relax/amber_minimize.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/amber_minimize.py +--- alphafold-2.3.2/alphafold/relax/amber_minimize.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/amber_minimize.py 2023-04-06 10:38:33.512754033 +0200 +@@ -27,10 +27,10 @@ + import ml_collections + import numpy as np + import jax +-from simtk import openmm +-from simtk import unit +-from simtk.openmm import app as openmm_app +-from simtk.openmm.app.internal.pdbstructure import PdbStructure ++from openmm import * ++from openmm import unit ++from openmm import app as openmm_app ++from openmm.app.internal.pdbstructure import PdbStructure + + + ENERGY = unit.kilocalories_per_mole +@@ -47,7 +47,7 @@ + + + def _add_restraints( +- system: openmm.System, ++ system: System, + reference_pdb: openmm_app.PDBFile, + stiffness: unit.Unit, + rset: str, +diff -ru alphafold-2.3.2/alphafold/relax/cleanup.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup.py +--- alphafold-2.3.2/alphafold/relax/cleanup.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup.py 2023-04-06 10:39:25.224888763 +0200 +@@ -20,8 +20,8 @@ + import io + + import pdbfixer +-from simtk.openmm import app +-from simtk.openmm.app import element ++from openmm import app ++from openmm.app import element + + + def fix_pdb(pdbfile, alterations_info): +diff -ru alphafold-2.3.2/alphafold/relax/cleanup_test.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup_test.py +--- alphafold-2.3.2/alphafold/relax/cleanup_test.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup_test.py 2023-04-06 10:39:58.409616942 +0200 +@@ -17,7 +17,7 @@ + + from absl.testing import absltest + from alphafold.relax import cleanup +-from simtk.openmm.app.internal import pdbstructure ++from openmm.app.internal import pdbstructure + + + def _pdb_to_structure(pdb_str): +diff -ru alphafold-2.3.2/docker/Dockerfile alphafold-2.3.2_use_openmm_7.7.0/docker/Dockerfile +--- alphafold-2.3.2/docker/Dockerfile 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/docker/Dockerfile 2023-04-06 10:41:10.315194781 +0200 +@@ -76,7 +76,6 @@ + + # Apply OpenMM patch. + WORKDIR /opt/conda/lib/python3.8/site-packages +-RUN patch -p0 < /app/alphafold/docker/openmm.patch + + # Add SETUID bit to the ldconfig binary so that non-root users can run it. + RUN chmod u+s /sbin/ldconfig.real +diff -ru alphafold-2.3.2/notebooks/AlphaFold.ipynb alphafold-2.3.2_use_openmm_7.7.0/notebooks/AlphaFold.ipynb +--- alphafold-2.3.2/notebooks/AlphaFold.ipynb 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/notebooks/AlphaFold.ipynb 2023-04-06 10:50:41.351746867 +0200 +@@ -103,16 +103,17 @@ + " %shell rm -rf /opt/conda\n", + " %shell wget -q -P /tmp \\\n", + " https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n", +- " \u0026\u0026 bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", +- " \u0026\u0026 rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ " && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", ++ " && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ + " pbar.update(9)\n", + "\n", + " PATH=%env PATH\n", + " %env PATH=/opt/conda/bin:{PATH}\n", + " %shell conda install -qy conda==4.13.0 \\\n", +- " \u0026\u0026 conda install -qy -c conda-forge \\\n", ++ " && conda install -qy -c conda-forge \\\n", + " python=3.9 \\\n", +- " openmm=7.5.1 \\\n", ++ " openmm=8.0.0 \\\n", + " pdbfixer\n", + " pbar.update(80)\n", + "\n", +@@ -164,8 +165,8 @@ + " pbar.update(10)\n", + "\n", + " # Apply OpenMM patch.\n", +- " %shell pushd /opt/conda/lib/python3.9/site-packages/ \u0026\u0026 \\\n", +- " patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n", ++ " %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n", ++ + " popd\n", + "\n", + " # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n", +@@ -189,9 +190,10 @@ + "\n", + "import jax\n", + "if jax.local_devices()[0].platform == 'tpu':\n", +- " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "elif jax.local_devices()[0].platform == 'cpu':\n", +- " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", ++ + "else:\n", + " print(f'Running with {jax.local_devices()[0].device_kind} GPU')\n", + "\n", +@@ -211,7 +213,7 @@ + "source": [ + "## Making a prediction\n", + "\n", +- "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ \u003e _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", ++ "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", + "\n", + "Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)." + ] +@@ -306,21 +308,21 @@ + "\n", + "# Check whether total length exceeds limit.\n", + "total_sequence_length = sum([len(seq) for seq in sequences])\n", +- "if total_sequence_length \u003e MAX_LENGTH:\n", ++ "if total_sequence_length > MAX_LENGTH:\n", + " raise ValueError('The total sequence length is too long: '\n", + " f'{total_sequence_length}, while the maximum is '\n", + " f'{MAX_LENGTH}.')\n", + "\n", + "# Check whether we exceed the monomer limit.\n", + "if model_type_to_use == ModelType.MONOMER:\n", +- " if len(sequences[0]) \u003e MAX_MONOMER_MODEL_LENGTH:\n", ++ " if len(sequences[0]) > MAX_MONOMER_MODEL_LENGTH:\n", + " raise ValueError(\n", + " f'Input sequence is too long: {len(sequences[0])} amino acids, while '\n", + " f'the maximum for the monomer model is {MAX_MONOMER_MODEL_LENGTH}. You may '\n", + " 'be able to run this sequence with the multimer model by selecting the '\n", + " 'use_multimer_model_for_monomers checkbox above.')\n", + " \n", +- "if total_sequence_length \u003e MAX_VALIDATED_LENGTH:\n", ++ "if total_sequence_length > MAX_VALIDATED_LENGTH:\n", + " print('WARNING: The accuracy of the system has not been fully validated '\n", + " 'above 3000 residues, and you may experience long running times or '\n", + " f'run out of memory. Total sequence length is {total_sequence_length} '\n", +@@ -421,7 +423,7 @@ + "]\n", + "\n", + "# Search UniProt and construct the all_seq features only for heteromers, not homomers.\n", +- "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " MSA_DATABASES.extend([\n", + " # Swiss-Prot and TrEMBL are concatenated together as UniProt.\n", + " {'db_name': 'uniprot',\n", +@@ -455,7 +457,7 @@ + " for sequence_index, sequence in enumerate(sorted(set(sequences)), 1):\n", + " fasta_path = f'target_{sequence_index:02d}.fasta'\n", + " with open(fasta_path, 'wt') as f:\n", +- " f.write(f'\u003equery\\n{sequence}')\n", ++ " f.write(f'>query\\n{sequence}')\n", + " sequence_to_fasta_path[sequence] = fasta_path\n", + "\n", + " # Run the search against chunks of genetic databases (since the genetic\n", +@@ -516,7 +518,7 @@ + " num_templates=0, num_res=len(sequence)))\n", + "\n", + " # Construct the all_seq features only for heteromers, not homomers.\n", +- " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " valid_feats = msa_pairing.MSA_FEATURES + (\n", + " 'msa_species_identifiers',\n", + " )\n", +@@ -680,7 +682,7 @@ + "banded_b_factors = []\n", + "for plddt in plddts[best_model_name]:\n", + " for idx, (min_val, max_val, _) in enumerate(PLDDT_BANDS):\n", +- " if plddt \u003e= min_val and plddt \u003c= max_val:\n", ++ " if plddt >= min_val and plddt <= max_val:\n", + " banded_b_factors.append(idx)\n", + " break\n", + "banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n", +@@ -693,14 +695,14 @@ + " f.write(relaxed_pdb)\n", + "\n", + "\n", +- "# --- Visualise the prediction \u0026 confidence ---\n", ++ "# --- Visualise the prediction & confidence ---\n", + "show_sidechains = True\n", + "def plot_plddt_legend():\n", + " \"\"\"Plots the legend for pLDDT.\"\"\"\n", +- " thresh = ['Very low (pLDDT \u003c 50)',\n", +- " 'Low (70 \u003e pLDDT \u003e 50)',\n", +- " 'Confident (90 \u003e pLDDT \u003e 70)',\n", +- " 'Very high (pLDDT \u003e 90)']\n", ++ " thresh = ['Very low (pLDDT < 50)',\n", ++ " 'Low (70 > pLDDT > 50)',\n", ++ " 'Confident (90 > pLDDT > 70)',\n", ++ " 'Very high (pLDDT > 90)']\n", + "\n", + " colors = [x[2] for x in PLDDT_BANDS]\n", + "\n", +@@ -816,13 +818,13 @@ + "id": "jeb2z8DIA4om" + }, + "source": [ +- "## FAQ \u0026 Troubleshooting\n", ++ "## FAQ & Troubleshooting\n", + "\n", + "\n", + "* How do I get a predicted protein structure for my protein?\n", + " * Click on the _Connect_ button on the top right to get started.\n", + " * Paste the amino acid sequence of your protein (without any headers) into the “Enter the amino acid sequence to fold”.\n", +- " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ \u003e _Run all._ Make sure you run all 5 cells in order.\n", ++ " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ > _Run all._ Make sure you run all 5 cells in order.\n", + " * The predicted protein structure will be downloaded once all cells have been executed. Note: This can take minutes to hours - see below.\n", + "* How long will this take?\n", + " * Downloading the AlphaFold source code can take up to a few minutes.\n", +@@ -831,8 +833,8 @@ + " * Running AlphaFold and generating the prediction can take minutes to hours, depending on the length of your protein and on which GPU-type Colab has assigned you.\n", + "* My Colab no longer seems to be doing anything, what should I do?\n", + " * Some steps may take minutes to hours to complete.\n", +- " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ \u003e _Restart runtime_.\n", +- " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ \u003e _Factory reset runtime_.\n", ++ " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ > _Restart runtime_.\n", ++ " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ > _Factory reset runtime_.\n", + "* How does this compare to the open-source version of AlphaFold?\n", + " * This Colab version of AlphaFold searches a selected portion of the BFD dataset and currently doesn’t use templates, so its accuracy is reduced in comparison to the full version of AlphaFold that is described in the [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and [Github repo](https://github.com/deepmind/alphafold/) (the full version is available via the inference script).\n", + "* What is a Colab?\n", +@@ -841,7 +843,7 @@ + " * The resources allocated to your Colab vary. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * You can execute the Colab nonetheless.\n", + "* I received an error “Colab CPU runtime not supported” or “No GPU/TPU found”, what do I do?\n", +- " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ \u003e _Change runtime type_ \u003e _Hardware accelerator_ \u003e _GPU_.\n", ++ " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ > _Change runtime type_ > _Hardware accelerator_ > _GPU_.\n", + " * The type of GPU allocated to your Colab varies. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * If you receive “Cannot connect to GPU backend”, you can try again later to see if Colab allocates you a GPU.\n", + " * [Colab Pro](https://colab.research.google.com/signup) offers priority access to GPUs.\n", From 78ec12f80a4b34741f8bc682ead15ac9fff20595 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 10:32:39 +0200 Subject: [PATCH 015/524] Add files via upload --- Kalign-3.4.0-GCCcore-12.3.0.eb | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 Kalign-3.4.0-GCCcore-12.3.0.eb diff --git a/Kalign-3.4.0-GCCcore-12.3.0.eb b/Kalign-3.4.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f6be972be5e --- /dev/null +++ b/Kalign-3.4.0-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +# Contribution from the NIHR Biomedical Research Centre +# update: THEMBL +easyblock = 'CMakeMake' + +name = 'Kalign' +version = '3.4.0' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['67d1a562d54b3b7622cc3164588c05b9e2bf8f1a5140bb48a4e816c61a87d4a8'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [], +} + +sanity_check_commands = ["kalign --help"] + +moduleclass = 'bio' From e25efa5bd3fe787d5a0d80bce02177a84c4c0507 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:08:31 +0200 Subject: [PATCH 016/524] Add files via upload --- dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb | 57 +++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb diff --git a/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a30f458a967 --- /dev/null +++ b/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +# update 0.9.11: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py + ('PyYAML', '6.0'), + ('CUDA', '12.1.1', '', SYSTEM), + ('tensorstore', '0.1.53'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('flax', '0.8.1', { + 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], + }), + ('optax', '0.1.9', { + 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], + }), + ('orbax_checkpoint', '0.5.3', { + 'modulename': 'orbax', + 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.85', { + 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From be544395eb74508cd9b9130cb9d09b8a0381d577 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:09:37 +0200 Subject: [PATCH 017/524] Add files via upload --- .../dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a30f458a967 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +# update 0.9.11: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py + ('PyYAML', '6.0'), + ('CUDA', '12.1.1', '', SYSTEM), + ('tensorstore', '0.1.53'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('flax', '0.8.1', { + 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], + }), + ('optax', '0.1.9', { + 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], + }), + ('orbax_checkpoint', '0.5.3', { + 'modulename': 'orbax', + 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.85', { + 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From dfdb612731c5e486d6d6558a1b3b914cb54b6fab Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:13:48 +0200 Subject: [PATCH 018/524] Add files via upload --- .../t/tensorstore-0.1.53-foss-2023a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb new file mode 100644 index 00000000000..0637b6107cb --- /dev/null +++ b/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb @@ -0,0 +1,62 @@ +# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'tensorstore' +version = '0.1.53' + +homepage = 'https://github.com/google/tensorstore' +description = """TensorStore is an open-source C++ and Python software library designed for +storage and manipulation of large multi-dimensional arrays.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('NASM', '2.16.01'), + ('pybind11', '2.11.1'), + ('Bazel', '6.3.1'), + + + + ('PyYAML', '6.0'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('snappy', '1.1.10'), + ('Brotli', '1.0.9'), + ('protobuf', '24.0'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('libwebp', '1.3.1'), + ('nlohmann_json', '3.11.2'), + ('Blosc', '1.21.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ml_dtypes', '0.3.2'), +] + +use_pip = True + + +local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" +local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" +local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? +local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" +local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" +# inject CFLAGS: +local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" + + +local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp + +exts_list = [ + (name, version, { + 'installopts': '-v', + 'preinstallopts': local_ts_preinstall, + 'checksums': ['45ef74b2dc9f2cd5f766bc373ded91d681cd021cc69d16592df48abaeb81af56'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From ecf79ffce68be6582289a1e4d529aad1059ffc05 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:15:09 +0200 Subject: [PATCH 019/524] Rename Kalign-3.4.0-GCCcore-12.3.0.eb to k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb --- .../Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename Kalign-3.4.0-GCCcore-12.3.0.eb => k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb (100%) diff --git a/Kalign-3.4.0-GCCcore-12.3.0.eb b/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb similarity index 100% rename from Kalign-3.4.0-GCCcore-12.3.0.eb rename to k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb From 3478d126cbc1af5796bd54ef265587490c8ee853 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:16:54 +0200 Subject: [PATCH 020/524] Rename k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb to easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb --- .../eeasyconfigs/k}/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {k => easybuild/eeasyconfigs/k}/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb (100%) diff --git a/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb b/easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb similarity index 100% rename from k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb rename to easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb From 4b2d49e54943270b5e772f728ee9ac794676ef8d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:19:15 +0200 Subject: [PATCH 021/524] Delete easybuild/eeasyconfigs/k/Kalign directory --- .../k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb diff --git a/easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb b/easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb deleted file mode 100644 index f6be972be5e..00000000000 --- a/easybuild/eeasyconfigs/k/Kalign/Kalign-3.4.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# update: THEMBL -easyblock = 'CMakeMake' - -name = 'Kalign' -version = '3.4.0' - -homepage = 'https://github.com/TimoLassmann/kalign' -description = "Kalign is a fast multiple sequence alignment program for biological sequences." - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['67d1a562d54b3b7622cc3164588c05b9e2bf8f1a5140bb48a4e816c61a87d4a8'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.26.3'), -] - -sanity_check_paths = { - 'files': ['bin/kalign'], - 'dirs': [], -} - -sanity_check_commands = ["kalign --help"] - -moduleclass = 'bio' From c8231bad74e92bae16959b7773849fe8f9eb4d61 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:22:14 +0200 Subject: [PATCH 022/524] Rename dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb to easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ --- .../d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb => easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ (100%) diff --git a/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ similarity index 100% rename from dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb rename to easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ From 66f01b38a697241e3d701ff307c93f5943483f65 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:23:04 +0200 Subject: [PATCH 023/524] Rename dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ to dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ --- .../d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/{eeasyconfigs => easyconfigs}/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ (100%) diff --git a/easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ similarity index 100% rename from easybuild/eeasyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ rename to easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ From d5d7bf5660c596c5f5ca96d6665292af739e8c72 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:25:30 +0200 Subject: [PATCH 024/524] Rename easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb to easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb --- .../t/{ => tensorstore}/tensorstore-0.1.53-foss-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/t/{ => tensorstore}/tensorstore-0.1.53-foss-2023a.eb (100%) diff --git a/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb similarity index 100% rename from easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb rename to easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb From 76bb632143d76dac75f303cbe1f6585aa600b5f0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:27:06 +0200 Subject: [PATCH 025/524] Delete easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ --- ...dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ deleted file mode 100644 index a30f458a967..00000000000 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb_ +++ /dev/null @@ -1,57 +0,0 @@ -# update 0.9.11: Thomas Hoffmann (EMBL) -easyblock = 'PythonBundle' - -name = 'dm-haiku' -version = '0.0.11' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://github.com/deepmind/dm-haiku' -description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural -network library for TensorFlow.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py - ('PyYAML', '6.0'), - ('CUDA', '12.1.1', '', SYSTEM), - ('tensorstore', '0.1.53'), - ('protobuf-python', '4.24.0'), -] - -use_pip = True - -exts_list = [ - ('jmp', '0.0.4', { - 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], - }), - ('flax', '0.8.1', { - 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], - }), - ('optax', '0.1.9', { - 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], - }), - ('orbax_checkpoint', '0.5.3', { - 'modulename': 'orbax', - 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], - }), - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('chex', '0.1.85', { - 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], - }), - ('nest_asyncio', '1.6.0', { - 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], - }), - (name, version, { - 'modulename': 'haiku', - 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From c78a22ade13ce1646520d32861fe5aeb3db12c53 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 21 Aug 2024 10:14:40 +0000 Subject: [PATCH 026/524] adding easyconfigs: Safetensors-0.4.4-gfbf-2023b.eb, tokenizers-0.19.1-GCCcore-13.2.0.eb, Transformers-4.44.0-gfbf-2023b.eb --- .../Safetensors-0.4.4-gfbf-2023b.eb | 153 +++++ .../Transformers-4.44.0-gfbf-2023b.eb | 36 ++ .../tokenizers-0.19.1-GCCcore-13.2.0.eb | 567 ++++++++++++++++++ 3 files changed, 756 insertions(+) create mode 100644 easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb new file mode 100644 index 00000000000..50ead1b54c1 --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -0,0 +1,153 @@ +easyblock = "CargoPythonBundle" + +name = 'Safetensors' +version = '0.4.4' +_rustver = '1.76.0' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast. + +This variant of Safetensors is installed with support for numpy and PyTorch +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('Rust', _rustver), + ('maturin', '1.5.0', '-Rust-' + _rustver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +# crates generated on 2024-08-21 from directories savetensors/ and bindings/python/ +crates = [ + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstyle', '1.0.8'), + ('autocfg', '1.3.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.16'), + ('clap_builder', '4.5.15'), + ('clap_lex', '0.7.2'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('either', '1.13.0'), + ('errno', '0.3.9'), + ('fastrand', '2.1.0'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.4.0'), + ('indoc', '2.0.5'), + ('is-terminal', '0.4.13'), + ('itertools', '0.10.5'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('libc', '0.2.158'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.14'), + ('log', '0.4.22'), + ('memchr', '2.7.4'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.4'), + ('plotters', '0.3.6'), + ('plotters-backend', '0.3.6'), + ('plotters-svg', '0.3.6'), + ('portable-atomic', '1.7.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.86'), + ('proptest', '1.5.0'), + ('pyo3', '0.22.2'), + ('pyo3-build-config', '0.22.2'), + ('pyo3-ffi', '0.22.2'), + ('pyo3-macros', '0.22.2'), + ('pyo3-macros-backend', '0.22.2'), + ('quick-error', '1.2.3'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rustix', '0.38.34'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('serde', '1.0.204'), + ('serde', '1.0.208'), + ('serde_derive', '1.0.204'), + ('serde_derive', '1.0.208'), + ('serde_json', '1.0.122'), + ('serde_json', '1.0.125'), + ('syn', '2.0.72'), + ('syn', '2.0.75'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.12.0'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('web-sys', '0.3.70'), + ('winapi-util', '0.1.9'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'checksums': ['5fe3e9b705250d0172ed4e100a811543108653fb2b66b9e702a088ad03772a07'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb new file mode 100644 index 00000000000..94a257d4b18 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.44.0' + +homepage = 'https://github.com/huggingface/transformers' +description = """State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('PyYAML', '6.0.1'), + ('tqdm', '4.66.2'), + ('tokenizers', '0.19.1'), # tokenizers>=0.19,<0.20 + ('Safetensors', '0.4.4'), # safetensors>=0.4.1 +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2024.7.24', { + 'checksums': ['9cfd009eed1a46b27c14039ad5bbc5e71b6367c5b2e6d5f5da0ea91600817506'], + }), + ('transformers', version, { + 'checksums': ['75699495e30b7635ca444d8d372e138c687ab51a875b387e33f1fb759c37f196'], + }), +] + +sanity_check_commands = [ + "python -c 'from transformers import AutoTokenizer'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3b5675b24df --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb @@ -0,0 +1,567 @@ +easyblock = 'CargoPythonBundle' + +name = 'tokenizers' +version = '0.19.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + ('adler2', '2.0.0'), + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.2.0'), + ('autocfg', '1.3.0'), + 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+builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.5.0', '-Rust-%s' % _rust_ver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # fsspec, filelock used by hf-hub + ('PyYAML', '6.0.1'), # used by hf-hub + ('tqdm', '4.66.2'), # used by hf-hub +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('huggingface-hub', '0.24.6', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['cc2579e761d070713eaa9c323e3debe39d5b464ae3a7261c39a9195b27bb8000'], + }), + (name, version, { + 'checksums': ['ee59e6680ed0fdbe6b724cf38bd70400a0c1dd623b07ac729087270caeac88e3'], + }), +] + +moduleclass = 'lib' From 11ad1c4225dace2bbfa1fdac424309d3d396e7e8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 26 Aug 2024 15:49:55 +0200 Subject: [PATCH 027/524] adding easyconfigs: NextDenovo-2.5.2-GCCcore-12.3.0.eb --- .../NextDenovo-2.5.2-GCCcore-12.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9d5cc1833bd --- /dev/null +++ b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'NextDenovo' +version = '2.5.2' + +homepage = 'https://github.com/Nextomics/NextDenovo' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextDenovo/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f1d07c9c362d850fd737c41e5b5be9d137b1ef3f1aec369dc73c637790611190'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextDenovo'] + +sanity_check_paths = { + 'files': ['nextDenovo', 'bin/minimap2-nd', 'bin/paralleltask', 'bin/nextgraph'], + 'dirs': ['bin', 'test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextDenovo --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' From 7d50d595e2ddf68e6dc00e4cda2d50bc920240f8 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 10:19:15 +0200 Subject: [PATCH 028/524] Added fmt in GCCcore-13.3.0 --- .../f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfb38383787 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '11.0.2' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['40fc58bebcf38c759e11a7bd8fdc163507d2423ef5058bba7f26280c5b9c5465'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 405fa19e5929da081d3b7fe3c8aba2403433a857 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 10:44:27 +0200 Subject: [PATCH 029/524] Added FLINT (plus dependency NTL) --- .../f/FLINT/FLINT-3.1.2-gfbf-2024a.eb | 45 +++++++++++++++++++ .../n/NTL/NTL-11.5.1-GCC-13.3.0.eb | 44 ++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb new file mode 100644 index 00000000000..970496a35d0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '3.1.2' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fdb3a431a37464834acff3bdc145f4fe8d0f951dd5327c4c6f93f4cbac5c2700'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('NTL', '11.5.1'), +] + +# Make flexiblas the first to be found and used to avoid linking openblas. +preconfigopts = 'sed -i "s/PATH_SUFFIXES openblas/PATH_SUFFIXES flexiblas openblas/g;' +preconfigopts += 's/accelerate openblas/accelerate flexiblas openblas/g" ' +preconfigopts += '%(builddir)s/%(namelower)s-%(version)s/CMake/FindCBLAS.cmake && ' + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..29fdd6e848f --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.38.2'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' From f1b6a3b561076ae191d19aee8f0e80a008af2d58 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 10:48:07 +0200 Subject: [PATCH 030/524] Added GEOS in GCC-13.3.0 and LERC in GCCcore-13.3.0 --- .../g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb | 22 +++++++++ .../l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..f409af68e96 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.12.2' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34c7770bf0090ee88488af98767d08e779f124fa33437e0aabec8abd4609fec6'] + +builddependencies = [('CMake', '3.29.3')] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos_c.so', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f4d5e9a50be --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DCMAKE_INSTALL_LIBDIR=lib' + +postinstallcmds = [ + # copy the LercTest source file to a LercTest subdir in the installation directory and compile it + # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "mkdir %(installdir)s/LercTest", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", + "cd %(installdir)s/LercTest && ${CXX} ${CXXFLAGS} main.cpp -o LercTest -I../include -L../lib -lLerc", +] + +sanity_check_commands = [ + "%(installdir)s/LercTest/LercTest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 523bc067dbf3a8fb00108d574c8659bd364fc61e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 10:58:43 +0200 Subject: [PATCH 031/524] Added libaio and libcerf in GCCcore-13.3.0 --- .../l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb | 39 +++++++++++++++++++ .../l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb | 32 +++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b76bc3cecc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.42')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2714c4d2765 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.4' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['080b30ae564c3dabe3b89264522adaf5647ec754021572bee54929697b276cdc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 343aca7b03aa2b49ded3d7127d6059a172ca1bb1 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 11:13:19 +0200 Subject: [PATCH 032/524] Added libcroco and libtirpc in GCCcore-13.3.0 --- .../libcroco-0.6.13-GCCcore-13.3.0.eb | 32 +++++++++++++++++++ .../libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb | 28 ++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..21b015fd6ed --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.13' + +homepage = 'https://gitlab.gnome.org/Archive/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libcroco/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['767ec234ae7aa684695b3a735548224888132e063f92db585759b422570621d4'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a9fc2a5d749 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.5' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['9b31370e5a38d3391bf37edfa22498e28fe2142467ae6be7a17c9068ec0bf12f'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 1689b901556de1a5f9c4a29fcefa34a50ba57c21 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 29 Aug 2024 11:23:25 +0200 Subject: [PATCH 033/524] Added libdap plus its dependency PCRE in GCCcore-13.3.0 --- .../libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb | 37 ++++++++++++++++ .../p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..707b32da095 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.21.0-27' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b5b8229d3aa97fea9bba4a0b11b1ee1c6446bd5f7ad2cff591f86064f465eacf'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('libxml2', '2.12.7'), + ('libtirpc', '1.3.5'), + ('PCRE', '8.45'), + ('util-linux', '2.40'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c378f2e1bab --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.%(namelower)s.org/pub/%(namelower)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +configopts = "--enable-utf --enable-unicode-properties --enable-pcre16 --enable-pcre32" + + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s-config', + 'include/%(namelower)s.h', + 'share/man/man3/%(namelower)s.3', + 'lib/libpcre32.%s' % SHLIB_EXT + ], + 'dirs': ['lib/pkgconfig', 'share/doc/%(namelower)s/html', 'share/man/man1'], +} + +moduleclass = 'devel' From 41a231dfa801762e360c2f597debb50554cefa7d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 29 Aug 2024 17:31:18 +0200 Subject: [PATCH 034/524] fix curl problem --- ...extDenovo-2.5.2-20240510-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e22a63378e9 --- /dev/null +++ b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'NextDenovo' +version = '2.5.2-20240510' +local_commit = '0e5fa5d' + +homepage = 'https://github.com/Nextomics/NextDenovo' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextDenovo/archive/'] +sources = [{'download_filename': '0e5fa5d.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['bbe43124e7d63cbe33179c2abf2de60797bb7361a7f7a2b5fc33bf62a4479726'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('cURL', '8.0.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextDenovo'] + +sanity_check_paths = { + 'files': ['nextDenovo', 'bin/minimap2-nd', 'bin/paralleltask', 'bin/nextgraph'], + 'dirs': ['bin', 'test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextDenovo --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' From 143050863328b831abc9008dc63ecadbf62d79f4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 29 Aug 2024 17:41:57 +0200 Subject: [PATCH 035/524] delete old version --- .../NextDenovo-2.5.2-GCCcore-12.3.0.eb | 52 ------------------- 1 file changed, 52 deletions(-) delete mode 100644 easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb deleted file mode 100644 index 9d5cc1833bd..00000000000 --- a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'MakeCp' - -name = 'NextDenovo' -version = '2.5.2' - -homepage = 'https://github.com/Nextomics/NextDenovo' -description = 'NextDenovo is a string graph-based de novo assembler for long reads.' - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/Nextomics/NextDenovo/archive/'] -sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['f1d07c9c362d850fd737c41e5b5be9d137b1ef3f1aec369dc73c637790611190'] - -builddependencies = [('binutils', '2.40')] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), -] - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, - 'preinstallopts': '', - 'installopts': '', -} - -exts_list = [ - ('Paralleltask', '0.2.3', { - 'modulename': 'paralleltask', - 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], - }), -] - -files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextDenovo'] - -sanity_check_paths = { - 'files': ['nextDenovo', 'bin/minimap2-nd', 'bin/paralleltask', 'bin/nextgraph'], - 'dirs': ['bin', 'test_data', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['nextDenovo --help'] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'PATH': '', -} - -moduleclass = 'bio' From 835f4109d8d591389a9cfab5f7943e3df4990367 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 29 Aug 2024 19:42:45 +0200 Subject: [PATCH 036/524] adding easyconfigs: SPRNG-5.0-gompi-2023b.eb, SPRNG-5.0-iimpi-2023b.eb, TestU01-1.2.3-GCCcore-13.2.0.eb and patches: SPRNG-5.0_MPI-lmpicxx.patch, SPRNG-5.0_MPI-lmpi.patch --- .../s/SPRNG/SPRNG-5.0-gompi-2023b.eb | 35 +++++++++++++++++++ .../s/SPRNG/SPRNG-5.0-iimpi-2023b.eb | 35 +++++++++++++++++++ .../s/SPRNG/SPRNG-5.0_MPI-lmpi.patch | 12 +++++++ .../s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch | 12 +++++++ .../t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb | 23 ++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch create mode 100644 easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb new file mode 100644 index 00000000000..bf9aa5e5827 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpi.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpi.patch': 'a6bb936b2e7cf9efd74e0bf06702bf444c98ecb11877492308a3551c5b9dff5c'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb new file mode 100644 index 00000000000..ea7f852cd44 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpicxx.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpicxx.patch': 'fc0903d81886a76a8cf2af73930b0347e3bcc047ad32215fdafd5a936f519545'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch new file mode 100644 index 00000000000..c09f74fa073 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:21:40.393998554 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpi" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch new file mode 100644 index 00000000000..a45691c9b04 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:18:56.124716693 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpicxx" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..08b769c2f8d --- /dev/null +++ b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'TestU01' +version = '1.2.3' + +homepage = 'https://simul.iro.umontreal.ca/testu01/tu01.html' +description = "Utilities for the empirical statistical testing of uniform random number generators" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://simul.iro.umontreal.ca/testu01/'] +sources = ['%(name)s.zip'] +checksums = ['bc1d1dd2aea7ed3b3d28eaad2c8ee55913f11ce67aec8fe4f643c1c0d2ed1cac'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/tcode', 'lib/libmylib.%s' % SHLIB_EXT, + 'lib/libprobdist.%s' % SHLIB_EXT, 'lib/libtestu01.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'share/TestU01/doc'], +} + +moduleclass = 'tools' From 07f7198fd3ee6d659d225ca403500430c51508d6 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 6 Sep 2024 18:58:23 +0200 Subject: [PATCH 037/524] adding easyconfigs: AOCC-4.2.0-GCCcore-13.3.0.eb --- .../a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a10c9e93da9 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +name = 'AOCC' +version = '4.2.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://download.amd.com/developer/eula/%(namelower)s/%(namelower)s-%(version_major)s-%(version_minor)s' +] +sources = ['%(namelower)s-compiler-%(version)s.tar'] +checksums = ['ed5a560ec745b24dc0685ccdcbde914843fb2f2dfbfce1ba592de4ffbce1ccab'] + +dependencies = [ + ('binutils', '2.42'), + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +clangversion = '16' + +moduleclass = 'compiler' From d2937b217572511ef1e2c6d66eb3f1a6a4323a2f Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 6 Sep 2024 22:06:50 +0200 Subject: [PATCH 038/524] Update AOCC-4.2.0-GCCcore-13.3.0.eb --- easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb index a10c9e93da9..864cac4d3ce 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb @@ -21,6 +21,6 @@ dependencies = [ ('libxml2', '2.12.7'), ] -clangversion = '16' +clangversion = '16.0.3' moduleclass = 'compiler' From a9a54ba6c29c6194bc2787c09bb0950a0c148d7c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 12 Sep 2024 16:30:22 +0200 Subject: [PATCH 039/524] Added binaries to Wannier90 module --- .../easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb index 9807690b35c..f8fe7f68bbf 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -25,10 +25,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } From 69ed20baf9748405a43c10db3bb16ceff2aafac9 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Sat, 14 Sep 2024 15:10:36 +0200 Subject: [PATCH 040/524] Now really added zsh, Xerces-C++, Voro++ and trimesh to the GCCcore-13.3.0 toolchain --- .../t/trimesh/trimesh-4.4.9-gfbf-2024a.eb | 33 ++++++++++++++ .../v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ .../Xerces-C++-3.2.5-GCCcore-13.3.0.eb | 39 +++++++++++++++++ .../z/zsh/zsh-5.9-GCCcore-13.3.0.eb | 30 +++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb new file mode 100644 index 00000000000..a25c1a4ac0f --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '4.4.9' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e9f54cb4ef70f9db49446cad3845b7a8043fc7d62d9192b241741f3fb0d813ac'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # numpy required +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9f6458281b3 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.42')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d9cb7a779c7 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.5' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['545cfcce6c4e755207bd1f27e319241e50e37c0c27250f11cda116018f1ef0f5'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('cURL', '8.7.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b396d28a23b --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' + +version = '5.9' + +homepage = 'http://www.zsh.org/' +description = """ +Zsh is a shell designed for interactive use, although it is also a powerful scripting language. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('ncurses', '6.5'), +] + +modextrapaths = { + 'FPATH': 'share/zsh/%(version)s/functions' +} + +moduleclass = 'tools' From 07fcd303aadd309d45821c0d10f84be891925258 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Sat, 14 Sep 2024 17:16:46 +0200 Subject: [PATCH 041/524] Added Szip to the GCCcore-13.3.0 toolchain and sympy to the gfbf-2024a toolchain --- .../s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb | 29 +++++++++++++++++++ .../s/sympy/sympy-1.13.2-gfbf-2024a.eb | 22 ++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..317db519350 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb new file mode 100644 index 00000000000..58034bd1d90 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb @@ -0,0 +1,22 @@ +name = 'sympy' +version = '1.13.2' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['401449d84d07be9d0c7a46a64bd54fe097667d5e7181bfe67ec777be9e01cb13'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('gmpy2', '2.2.0'), +] + + +moduleclass = 'math' From fe04ce2d20a9b15bc3dc50454c39e33de373471b Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Sat, 14 Sep 2024 18:53:14 +0200 Subject: [PATCH 042/524] Added Suitesparse to the foss-2024a toolchain. --- ...uiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb new file mode 100644 index 00000000000..7bcd3143b6f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '7.8.2' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['996c48c87baaeb5fc04bd85c7e66d3651a56fe749c531c60926d75b4db5d2181'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.1'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 6d51bd667e619c62716eec30c0970a5f394302af Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 16 Sep 2024 08:28:30 +0200 Subject: [PATCH 043/524] Added Sox (plus dep libmad) to the GCCcore-13.3.0 toolchain --- .../l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb | 27 +++++++++++++++ .../s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..982f59275b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libmad' +version = '0.15.1b' + +homepage = 'https://www.underbit.com/products/mad/' +description = """MAD is a high-quality MPEG audio decoder.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch'] +checksums = [ + 'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690', # libmad-0.15.1b.tar.gz + # libmad-0.15.1b-remove-depreciated-gcc-option.patch + '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678', +] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'lib64'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..747709683fb --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://sox.sourceforge.net/' +docurls = 'http://sox.sourceforge.net/Docs/Documentation' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('FLAC', '1.4.3'), + ('LAME', '3.100'), + ('libmad', '0.15.1b'), + ('libvorbis', '1.3.7'), + ('FFmpeg', '7.0.2'), +] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/rec', 'bin/sox', 'bin/soxi', 'include/sox.h', + 'lib/libsox.la', 'lib/libsox.a', 'lib/pkgconfig/sox.pc', 'lib/libsox.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], +} + +sanity_check_commands = ['sox --help'] + +moduleclass = 'data' From cf28c59088f9a7833c5f25b4cd2a3a4f16650aea Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 16 Sep 2024 12:09:41 +0200 Subject: [PATCH 044/524] Added at-spi2-core and at-spi2-atk to the GCCcore-13.3.0 toolchain. --- .../at-spi2-atk-2.38.0-GCCcore-13.3.0.eb | 37 +++++++++++++++++ .../at-spi2-core-2.54.0-GCCcore-13.3.0.eb | 40 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6efc7996fd0 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('DBus', '1.15.8'), + ('at-spi2-core', '2.54.0'), + ('libxml2', '2.12.7'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b1a1a4c863f --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.54.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d7eee7e75beddcc272cedc2b60535600f3aae6e481589ebc667afc437c0a6079'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('DBus', '1.15.8'), + ('X11', '20240607'), +] + +# Hard disable Dbus broker detection and (potential) use of systemd +configopts = "--libdir lib -Duse_systemd=false -Ddefault_bus=dbus-daemon" + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From e2a8fc8f60155a49f229e62782780fcfba4a3ea2 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 16 Sep 2024 12:31:50 +0200 Subject: [PATCH 045/524] Added inih and exiv2 to the GCCcore-13.3.0 toolchain. --- .../e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb | 38 +++++++++++++++++++ .../i/inih/inih-58-GCCcore-13.3.0.eb | 30 +++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fba04816180 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.28.3' + +homepage = 'http://www.exiv2.org' +description = """ + Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write + access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and + with a commercial license, and is used in many projects. +""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Exiv2/exiv2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1315e17d454bf4da3cc0edb857b1d2c143670f3485b537d0f946d9ed31d87b70'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('expat', '2.6.2'), + ('Brotli', '1.1.0'), + ('inih', '58'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["exiv2 --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0837277c267 --- /dev/null +++ b/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'inih' +version = '58' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/benhoyt/inih/archive/refs/tags/'] +sources = ['r%(version)s.tar.gz'] +checksums = ['e79216260d5dffe809bda840be48ab0eec7737b2bb9f02d2275c1b46344ea7b7'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +# installing manpages requires an extra build dependency (docbook xsl) +# configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libinih.%s' % SHLIB_EXT, 'include/ini.h'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' From 97820235323028049a94c9420b4d0b263e1b35b3 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 16 Sep 2024 16:29:14 +0200 Subject: [PATCH 046/524] Added GraphicsMagick and HDF to the GCCcore-13.3.0 toolchain. --- .../GraphicsMagick-1.3.45-GCCcore-13.3.0.eb | 51 ++++++++++++++++ .../h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb | 58 +++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..63340e41506 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.45' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_XZ] +patches = [ + 'GraphicsMagick_pkgconfig_libtiff.patch' +] +checksums = [ + {'GraphicsMagick-1.3.45.tar.xz': 'dcea5167414f7c805557de2d7a47a9b3147bcbf617b91f5f0f4afe5e6543026b'}, + {'GraphicsMagick_pkgconfig_libtiff.patch': '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('X11', '20240607'), + ('bzip2', '1.0.8'), + ('freetype', '2.13.2'), + ('libpng', '1.6.43'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('libxml2', '2.12.7'), + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), + ('Ghostscript', '10.03.1'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +sanity_check_paths = { + 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', + 'lib/libGraphicsMagickWand.a'], + 'dirs': ['include/GraphicsMagick', 'lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de3ac32380a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.3.0' + +homepage = 'https://support.hdfgroup.org/products/hdf4/' +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/HDFGroup/hdf4/archive/refs/tags/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['a6639a556650e6ea8632a17b8188a69de844bdff54ce121a1fd5b92c8dd06cb1'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Szip', '2.1.1'), + ('zlib', '1.3.1'), + ('libtirpc', '1.3.5'), +] + +preconfigopts = "LIBS='-ltirpc' " + +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +configopts = [ + local_common_configopts, + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'data' From dd8c56dee9f9685999d1442011fc0636e6a21a19 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 17 Sep 2024 09:17:46 +0200 Subject: [PATCH 047/524] Added IPython (plus dep jedi) to the GCCcore-13.3.0 toolchain. --- .../IPython/IPython-8.27.0-GCCcore-13.3.0.eb | 80 +++++++++++++++++++ .../j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb | 37 +++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.27.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.27.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.27.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a85e58910e9 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.27.0-GCCcore-13.3.0.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.27.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ZeroMQ', '4.3.5'), + ('lxml', '5.3.0'), + ('jedi', '0.19.1') +] + +sanity_pip_check = True +use_pip = True + +# for the matplotlib-inline required extention we avoid the import sanity check +# as it will fail without matplotlib in the environment, but ipython devs prefer not to make +# matplotlib a required dep (https://github.com/ipython/matplotlib-inline/issues/4) +# we follow the same convention and we not set matplotlib as dependency + +# Last updated 20240917 +exts_list = [ + ('traitlets', '5.14.3', { + 'checksums': ['9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7'], + }), + ('pure_eval', '0.2.3', { + 'checksums': ['5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42'], + }), + ('executing', '2.1.0', { + 'checksums': ['8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab'], + }), + ('asttokens', '2.4.1', { + 'checksums': ['b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0'], + }), + ('stack_data', '0.6.3', { + 'checksums': ['836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9'], + }), + ('prompt_toolkit', '3.0.47', { + 'checksums': ['1e1b29cb58080b1e69f207c893a1a7bf16d127a5c30c9d17a25a5d77792e5360'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('matplotlib-inline', '0.1.6', { + 'modulename': False, + 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['0b99a2dc9f15fd68692e898e5568725c6d49c527d36a9fb5960ffbdeaa82ff7e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c4d7702a368 --- /dev/null +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'jedi' +version = "0.19.1" + +homepage = 'https://github.com/davidhalter/jedi' +description = """ + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('parso', '0.8.4', { + 'checksums': ['eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d'], + }), + (name, version, { + 'checksums': ['cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.12/site-packages/jedi'], +} + +moduleclass = 'tools' From 0379ec895de51d5fb31f042028d7875fea9896ed Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 18 Sep 2024 09:04:24 +0200 Subject: [PATCH 048/524] Added libgeotiff to the GCCcore-13.3.0 toolchain. --- .../libgeotiff-1.7.3-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..41cba249999 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.3' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba23a3a35980ed3de916e125c739251f8e3266be07540200125a307d7cf5a704'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('PROJ', '9.4.1'), + ('libjpeg-turbo', '3.0.1'), + ('zlib', '1.3.1'), + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 7a93121522fe5dfb4144648158d9004bef49b675 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 19 Sep 2024 20:33:24 +0200 Subject: [PATCH 049/524] Added the sanity check paths and sanity check command to the zsh easyconfig file. --- easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb index b396d28a23b..2ddb0b4f403 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb @@ -27,4 +27,11 @@ modextrapaths = { 'FPATH': 'share/zsh/%(version)s/functions' } +sanity_check_paths = { + 'files': ['bin/zsh'], + 'dirs': ['lib/zsh/%(version)s', 'share'], +} + +sanity_check_commands = ['zsh --version'] + moduleclass = 'tools' From 16863d05e4cbe2faa6f57ab5119638166473f601 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 23 Sep 2024 19:39:34 +0200 Subject: [PATCH 050/524] Change description --- easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb index 864cac4d3ce..b88337b09b4 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb @@ -2,7 +2,10 @@ name = 'AOCC' version = '4.2.0' homepage = 'https://developer.amd.com/amd-aocc/' -description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" +description = """AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages. + It supports target-dependent and target-independent optimizations. It is highly optimized for x86 targets, + especially for AMD “Zen”-based processors giving a performance edge for time critical HPC and other + applications over other compilers.""" # Clang also depends on libstdc++ during runtime, but this dependency is # already specified as the toolchain. From fe1d7d50fb0d777a7d14bac349e5a77d387f6c5a Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 1 Oct 2024 14:09:21 +0200 Subject: [PATCH 051/524] adding easyconfigs: VTune-2024.3.0.eb --- .../easyconfigs/v/VTune/VTune-2024.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb new file mode 100644 index 00000000000..850f62f204a --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb @@ -0,0 +1,25 @@ + +name = 'VTune' +version = '2024.3.0' + +homepage = 'https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html' +description = """Intel® VTune™ Profiler optimizes application performance, system performance, + and system configuration for HPC, cloud, IoT, media, storage, and more.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfae6f23-6c90-4b9f-80e2-fa2a5037fe36/'] +sources = ['l_oneapi_vtune_p_%(version)s.31_offline.sh'] +checksums = ['da9f45ee4a5ea337756e85e58e40b235417cffbca6813cf224db49061947253d'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' From 9987d7e2d1ec6c2f6c2b72ccc8b60d1f994c8e2b Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 1 Oct 2024 16:21:36 +0100 Subject: [PATCH 052/524] adding easyconfigs: HDF5-1.14.5-iimpi-2024a.eb, Szip-2.1.1-GCCcore-13.3.0.eb --- .../h/HDF5/HDF5-1.14.5-iimpi-2024a.eb | 26 +++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb | 29 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb new file mode 100644 index 00000000000..153463a2234 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/HDFGroup/hdf5/archive'] +sources = ['hdf5_%(version)s.tar.gz'] +checksums = ['c83996dc79080a34e7b5244a1d5ea076abfd642ec12d7c25388e2fdd81d26350'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.3.1'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5d0c22c87b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://docs.hdfgroup.org/archive/support/doc_resource/SZIP/index.html' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From 37337a5c836747184617014d4f9d2cd3d6359a6d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 1 Oct 2024 17:15:21 +0100 Subject: [PATCH 053/524] Binutils version corrected --- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb index 5d0c22c87b4..6ac6fb2e784 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] builddependencies = [ - ('binutils', '2.40'), + ('binutils', '2.42'), ] sanity_check_paths = { From c84acefcb93ab1e74659cd7b35ba11f5bf082369 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 2 Oct 2024 14:40:33 +0200 Subject: [PATCH 054/524] Fixed download URL --- easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb index 850f62f204a..a7340fe52b8 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfae6f23-6c90-4b9f-80e2-fa2a5037fe36/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/d7e1fdb1-cfc7-40fb-bf46-3719e9372d67/'] sources = ['l_oneapi_vtune_p_%(version)s.31_offline.sh'] checksums = ['da9f45ee4a5ea337756e85e58e40b235417cffbca6813cf224db49061947253d'] From 3a8ed87051ae429a8307c67f3021d614cdaac65b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 2 Oct 2024 14:42:38 +0200 Subject: [PATCH 055/524] GTDB-Tk v2.4.0 should use skani and not FastANI --- .../g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb | 2 +- .../s/skani/skani-0.2.2-GCCcore-12.3.0.eb | 481 ++++++++++++++++++ 2 files changed, 482 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb index 271be65a5dd..a8f48c5966b 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb @@ -19,7 +19,7 @@ dependencies = [ ('prodigal', '2.6.3'), ('HMMER', '3.4'), ('pplacer', '1.1.alpha19', '', SYSTEM), - ('FastANI', '1.34'), + ('skani', '0.2.2'), ('FastTree', '2.1.11'), ('Mash', '2.3'), ('tqdm', '4.66.1'), diff --git a/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..889947f5c2c --- /dev/null +++ b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,481 @@ +easyblock = 'Cargo' + +name = 'skani' +version = '0.2.2' + +homepage = 'https://github.com/bluenote-1577/skani' +description = "skani - accurate, fast nucleotide identity calculation for MAGs, genomes, and databases" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'bluenote-1577' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.2.2.tar.gz': 'e047d52b9f753625eff480fe90f1abb68f82cc6892d9d1910b18bfcedbfc0b9d'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'anyhow-1.0.75.tar.gz': 'a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6'}, + {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'}, + {'assert_cmd-1.0.8.tar.gz': 'c98233c6673d8601ab23e77eb38f999c51100d46c5703b17288c57fddf3a1ffe'}, + {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'}, + {'autocfg-0.1.8.tar.gz': 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'9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wide-0.7.12.tar.gz': 'ebecebefc38ff1860b4bc47550bbfa63af5746061cf0d29fcd7fa63171602598'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), +] + +# Since we do the download of partitions, remove the download part from skani +prebuildopts = """sed -i -e 's/^partitions = {/#&/' -e 's/^#partitions = ".*/partitions = "0.2.4"/' Cargo.toml && """ + +crates = [ + ('adler', '1.0.2'), + ('aho-corasick', '1.1.2'), + ('anyhow', '1.0.75'), + ('approx', '0.5.1'), + ('assert_cmd', '1.0.8'), + ('atty', '0.2.14'), + ('autocfg', '0.1.8'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bio', '1.4.0'), + ('bio-types', '1.0.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.5.1'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.0'), + ('bstr', '0.2.17'), + ('buffer-redux', '1.0.0'), + ('bv', '0.11.1'), + ('bytecount', '0.6.4'), + ('bytemuck', '1.14.0'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.83'), + ('cfg-if', '0.1.10'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cloudabi', '0.0.3'), + ('crc32fast', '1.3.2'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('custom_derive', '0.1.7'), + ('dashmap', '5.5.3'), + ('derive-new', '0.5.9'), + ('difference', '2.0.0'), + ('difflib', '0.4.0'), + ('doc-comment', '0.3.3'), + ('editdistancek', '1.0.2'), + ('either', '1.9.0'), + ('enum-map', '1.1.1'), + ('enum-map-derive', '0.6.0'), + ('equivalent', '1.0.1'), + ('errno', '0.3.5'), + ('fastrand', '1.9.0'), + ('fastrand', '2.0.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.27'), + ('float-cmp', '0.8.0'), + ('fnv', '1.0.7'), + ('fuchsia-cprng', '0.1.1'), + ('futures', '0.3.28'), + ('futures-channel', '0.3.28'), + ('futures-core', '0.3.28'), + ('futures-executor', '0.3.28'), + ('futures-io', '0.3.28'), + ('futures-sink', '0.3.28'), + ('futures-task', '0.3.28'), + ('futures-util', '0.3.28'), + ('fxhash', '0.2.1'), + ('gbdt', '0.1.1'), + ('gcollections', '1.5.0'), + ('getrandom', '0.2.10'), + ('getset', '0.1.2'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.1.19'), + ('indexed', '0.1.1'), + ('indexmap', '1.9.3'), + ('indexmap', '2.0.2'), + ('instant', '0.1.12'), + ('intervallum', '1.4.0'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.9'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.149'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.10'), + ('lock_api', '0.4.10'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.6.4'), + ('memoffset', '0.9.0'), + ('miniz_oxide', '0.7.1'), + ('multimap', '0.8.3'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('normalize-line-endings', '0.3.0'), + ('num-complex', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.17'), + ('once_cell', '1.18.0'), + ('ordered-float', '3.9.1'), + ('os_str_bytes', '6.5.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('partitions', '0.2.4'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pin-project-lite', '0.2.13'), + ('pin-utils', '0.1.0'), + ('pkg-config', '0.3.27'), + ('ppv-lite86', '0.2.17'), + ('predicates', '1.0.8'), + ('predicates', '2.1.5'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '0.2.3'), + ('proc-macro2', '1.0.69'), + ('proptest', '0.8.7'), + ('quick-error', '1.2.3'), + ('quote', '0.4.2'), + ('quote', '1.0.33'), + ('rand', '0.5.6'), + ('rand', '0.6.5'), + ('rand', '0.8.5'), + ('rand_chacha', '0.1.1'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rand_hc', '0.1.0'), + ('rand_isaac', '0.1.1'), + ('rand_jitter', '0.1.4'), + ('rand_os', '0.1.3'), + ('rand_pcg', '0.1.2'), + ('rand_xorshift', '0.1.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.8.0'), + ('rayon-core', '1.12.0'), + ('rdrand', '0.4.0'), + ('redox_syscall', '0.1.57'), + ('redox_syscall', '0.3.5'), + ('reflection', '0.1.3'), + ('reflection_derive', '0.1.1'), + ('regex', '1.10.0'), + ('regex-automata', '0.1.10'), + ('regex-automata', '0.4.1'), + ('regex-syntax', '0.6.29'), + ('regex-syntax', '0.8.0'), + ('rust-lapper', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustix', '0.38.18'), + ('rustversion', '1.0.14'), + ('rusty-fork', '0.2.2'), + ('ryu', '1.0.15'), + ('safe_arch', '0.7.1'), + ('safemem', '0.3.3'), + ('scopeguard', '1.2.0'), + ('semver', '0.1.20'), + ('serde', '1.0.188'), + ('serde_derive', '1.0.188'), + ('serde_derive_internals', '0.21.0'), + ('serde_json', '1.0.107'), + ('serial_test', '0.10.0'), + ('serial_test_derive', '0.10.0'), + ('simba', '0.6.0'), + ('simple-logging', '2.0.2'), + ('slab', '0.4.9'), + ('smallvec', '1.11.1'), + ('statrs', '0.16.0'), + ('strsim', '0.10.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.2'), + ('syn', '0.12.15'), + ('syn', '1.0.109'), + ('syn', '2.0.38'), + ('tempfile', '3.8.0'), + ('termcolor', '1.3.0'), + ('termtree', '0.4.1'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.49'), + ('thiserror-impl', '1.0.49'), + ('thread-id', '3.3.0'), + ('tikv-jemalloc-sys', '0.5.4+5.3.0-patched'), + ('tikv-jemallocator', '0.5.4'), + ('trees', '0.2.1'), + ('trilean', '1.1.0'), + ('triple_accel', '0.4.0'), + ('tsv', '0.1.1'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.1.0'), + ('vec_map', '0.8.2'), + ('version_check', '0.9.4'), + ('wait-timeout', '0.2.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.12'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), + ('xz2', '0.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/skani'], + 'dirs': [], +} + +sanity_check_commands = [ + 'skani --help', +] + + +moduleclass = 'bio' From 8da80bf530d749a26d46b26fe72c795cae49e080 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 3 Oct 2024 08:21:13 +0200 Subject: [PATCH 056/524] adding easyconfigs: PyBerny-0.6.3-foss-2023a.eb --- .../p/PyBerny/PyBerny-0.6.3-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb new file mode 100644 index 00000000000..71cb5554837 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyBerny' +version = '0.6.3' + +homepage = 'https://github.com/jhrmnn/pyberny' +description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, +using nuclear gradient information.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('pyberny', version, { + 'modulename': 'berny', + 'checksums': ['b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/berny'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["berny -h"] + +moduleclass = 'chem' From 687f6465a0bd48188e40d8cb3f7d586764183eb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 3 Oct 2024 08:22:46 +0200 Subject: [PATCH 057/524] adding easyconfigs: PyCheMPS2-1.8.12-foss-2023a.eb --- .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb new file mode 100644 index 00000000000..222a89010a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyCheMPS2' +version = '1.8.12' + +homepage = 'https://sebwouters.github.io/CheMPS2' +description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without +MPI. CheMPS2 is a scientific library which contains a spin-adapted +implementation of the density matrix renormalization group (DMRG) +for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], + 'install_src': './%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' From 58a2fe72c290fc044b99f7a92f7e545bc057cfb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 3 Oct 2024 08:25:17 +0200 Subject: [PATCH 058/524] adding easyconfigs: Block-1.5.3-20200525-foss-2023a.eb --- .../Block/Block-1.5.3-20200525-foss-2023a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb new file mode 100644 index 00000000000..da1316c8aa6 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'MakeCp' + +name = 'Block' +version = '1.5.3-20200525' +_commit = 'f95317b08043b7c531289576d59ad74a6d920741' + +homepage = 'https://sanshar.github.io/Block/' +description = """Block implements the density matrix renormalization group (DMRG) algorithm for +quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++11', 'pic': True} + +# Version 1.5 is a major rewrite of Block that was named at some point StackBlock +# sources are available in sanshar/StackBlock +# sources at sanshar/Block@b0e3671aad and pyscf/Block@db27636b76 correspond to version 1.1.1 +source_urls = ['https://github.com/sanshar/StackBlock/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = [ + 'Block-1.5.3_use-eb-environment.patch', + 'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch', + 'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch' +] +checksums = [ + {'1.5.3-20200525.tar.gz': '8d793c5e460d7747a0adcb06ce4b457c6750cf2d42cead1d060db8b44643c3b1'}, + {'Block-1.5.3_use-eb-environment.patch': '7f3e8a52f28d251441d20dfde1f9cb8cdc0c34216defab61cc6980e540a6cf60'}, + {'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch': + 'f53f1f88cb7b12ab38d1313f93a9bbd31c745dca1beca7a8d51d00e0ae4e762f'}, + {'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch': + '51d692f294e800e0a9e027ef35bf761612ecb9efe77ddb378ec973b55e39a1e8'}, +] + +dependencies = [ + ('Boost.MPI', '1.82.0'), +] + +buildopts = [ + # Multi-threaded build (block.spin_adapted-serial) + 'OPENMP="yes" EXECUTABLE="block.spin_adapted-serial"', + # MPI build (block.spin_adapted) + 'USE_MPI="yes"', +] + +files_to_copy = [(['block.spin_adapted*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], + 'dirs': [], +} + +sanity_check_commands = [ + "block.spin_adapted-serial --version", + "%(mpi_cmd_prefix)s block.spin_adapted --version", +] + +moduleclass = 'phys' From 0a1e4603bf9c8afbba9954105a0ce7ec5f0fde8e Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Thu, 3 Oct 2024 15:47:08 +0100 Subject: [PATCH 059/524] adding easyconfigs: CASTEP-24.1-foss-2023b.eb --- .../c/CASTEP/CASTEP-24.1-foss-2023b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb new file mode 100644 index 00000000000..678f4e7df25 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '24.1' + +homepage = 'http://www.castep.org' +description = """ +CASTEP is an electronic structure materials modelling code based on density +functional theory (DFT), with functionality including geometry optimization +molecular dynamics, phonons, NMR chemical shifts and much more. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use +only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['97d77a4f3ce3f5c5b87e812f15a2c2cb23918acd7034c91a872b6d66ea0f7dbb'] + +dependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for elastic constants and castepconv utility +] + +skipsteps = ['configure'] + +_generic_opts = ' COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" ' + +buildopts = _generic_opts + 'FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin &&' +installopts = _generic_opts + 'INSTALL_DIR="%(installdir)s/bin"' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + +sanity_check_commands = [ + 'castep.mpi --help', + 'optados.mpi --help', +] + +moduleclass = 'phys' From 0ad9dd9c7e1bd4f412bb015d62e0795afd29d3c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:30:47 +0200 Subject: [PATCH 060/524] {lib}[GCCcore/13.3.0] Add NCCL 2.22.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..0534e538faa --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,26 @@ +name = 'NCCL' +version = '2.22.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['45151629a9494460e73375281e8b0fe379141528879301899ece9b776faca024'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +moduleclass = 'lib' From 01c1b0484b84331c7d8d9d83ca50ea3c64ca09c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:31:29 +0200 Subject: [PATCH 061/524] {lib}[GCCcore/13.3.0] Add UCC-CUDA 1.3.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- ...C-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb | 55 +++++++++++++++++++ ...1.3.0_link_against_existing_UCC_libs.patch | 27 +++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a0b4865a721 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', +] +checksums = [ + {'v1.3.0.tar.gz': 'b56379abe5f1c125bfa83be305d78d81a64aa271b7b5fff0ac17b86725ff3acf'}, + {'UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch': + '758228357ce2a6ae50fb26a0b43e9176feaf379e266365f38205ce679267fc0d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('NCCL', '2.22.3', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch new file mode 100644 index 00000000000..5d005e067f7 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch @@ -0,0 +1,27 @@ +Make CUDA/NCCL plugins link against the existing ucc libraries. + +Bart Oldeman, 2022-08-02 +Mikael OEhman, 2023-06-16 +diff -ur ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am ucc-1.3.0/src/components/ec/cuda/Makefile.am +--- ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am.orig 2023-06-16 12:56:53.205939925 +0200 ++++ ucc-1.3.0/src/components/mc/cuda/Makefile.am 2023-06-16 13:02:21.716110609 +0200 +@@ -14,7 +14,7 @@ + libucc_mc_cuda_la_CFLAGS = $(BASE_CFLAGS) + libucc_mc_cuda_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) + libucc_mc_cuda_la_LIBADD = $(CUDA_LIBS) \ +- $(UCC_TOP_BUILDDIR)/src/libucc.la ++ -lucc + + include $(top_srcdir)/config/module.am + endif +diff -ur ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am ucc-1.0.0/src/components/tl/nccl/Makefile.am +--- ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/tl/nccl/Makefile.am 2022-08-02 12:13:59.334795989 +0000 +@@ -21,6 +21,6 @@ + libucc_tl_nccl_la_CPPFLAGS = $(AM_CPPFLAGS) $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(NCCL_CPPFLAGS) + libucc_tl_nccl_la_CFLAGS = $(BASE_CFLAGS) + libucc_tl_nccl_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) $(NCCL_LDFLAGS) +-libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) $(UCC_TOP_BUILDDIR)/src/libucc.la ++libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) -lucc + + include $(top_srcdir)/config/module.am From fb92d714a597135d8818b1255b49d151edaa9bde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 4 Oct 2024 17:30:55 +0200 Subject: [PATCH 062/524] adding easyconfigs: GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb --- .../GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..ebc1ba1601a --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,91 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 571dbd1247a84dab794de5cee138a73f97e9d509 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 4 Oct 2024 19:30:01 +0200 Subject: [PATCH 063/524] adding easyconfigs: Dice-20240702-foss-2023a.eb --- .../d/Dice/Dice-20240702-foss-2023a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb b/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb new file mode 100644 index 00000000000..56756b3f99f --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'Dice' +version = '20240702' +_commit = '0f52b62' + +homepage = 'https://github.com/sanshar/Dice' +description = """Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI +and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++14', 'pic': True} + +github_account = 'sanshar' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Dice-20240101_deprecated-global-placeholders.patch'] +checksums = [ + {'Dice-20240702.tar.gz': '3fe36938642ebf7886231290655c1a2d1fdd256e2bc7e9375669c574c406fc23'}, + {'Dice-20240101_deprecated-global-placeholders.patch': + 'fbf4037e928a57e737faed95dc7d6e1e5cdb8cee8db48503268d250a34c12ccc'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Boost.MPI', '1.82.0'), + ('HDF5', '1.14.0'), +] + +# Use build environment defined by EB +prebuildopts = "sed -i 's/^FLAGS_BASE =.*/FLAGS_BASE=$(CXXFLAGS) -g -w -I. $(CPPFLAGS)/' Makefile && " +buildopts = 'CXX="$MPICXX" USE_INTEL="no" HAS_AVX2="no" ' # avoid changes to -march +buildopts += 'INCLUDE_MKL="-I${EBROOTFLEXIBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use FlexiBLAS +buildopts += 'GIT_BRANCH="master" GIT_HASH="%s"' % _commit +buildopts += 'BOOST="${EBROOTBOOSTMPI}" ' +buildopts += 'EIGEN="${EBROOTEIGEN}/include" ' +buildopts += 'HDF5="${EBROOTHDF5}" ' + +files_to_copy = ['bin'] + +_binaries = ['Dice', 'DQMC', 'GFMC', 'ICPT', 'VMC', 'ZDice2', 'ZSHCI'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'chem' From d7669298d55856294a64ab415326d339eb9ffd89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 4 Oct 2024 23:09:22 +0200 Subject: [PATCH 064/524] adding easyconfigs: KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb, numpy-1.16.6-foss-2023a-Python-2.7.18.eb, pytest-4.6.11-foss-2023a-Python-2.7.18.eb and patches: numpy-1.16.2_relax-long-complex-test.patch, numpy-1.16.6_add_flexiblas_detection.patch, numpy-1.16.6_handle_failing_linalg_test.patch, numpy-1.20.3_fix-fortran-compiler-error.patch --- .../KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb | 51 +++++ ...numpy-1.16.2_relax-long-complex-test.patch | 17 ++ .../numpy-1.16.6-foss-2023a-Python-2.7.18.eb | 37 ++++ ...numpy-1.16.6_add_flexiblas_detection.patch | 181 ++++++++++++++++++ ...py-1.16.6_handle_failing_linalg_test.patch | 17 ++ ...py-1.20.3_fix-fortran-compiler-error.patch | 43 +++++ .../pytest-4.6.11-foss-2023a-Python-2.7.18.eb | 87 +++++++++ 7 files changed, 433 insertions(+) create mode 100644 easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..77d18cbdc50 --- /dev/null +++ b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'KMCLib' +version = '2.0-a2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/leetmaa/KMCLib' +description = """KMCLib - a general framework for lattice kinetic Monte Carlo (KMC) simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/leetmaa/KMCLib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['796620a67ad010df4b11734f703151c17441f82cef026f3d56386a34056d0213'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('numpy', '1.16.6', versionsuffix), + ('SWIG', '4.1.1'), +] + +start_dir = 'c++' + +preconfigopts = 'cd ../%(name)s-%(version)s/c++/externals && ' +preconfigopts += 'make CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" && cd - && ' + +prebuildopts = 'export CPATH=$EBROOTPYTHON/include/python%(pyshortver)s:$CPATH && ' + +postinstallcmds = [ + 'cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s"', + 'cp -r "%(builddir)s/../python/src/KMCLib/Backend/"* "%(installdir)s/KMCLib/Backend/"', +] + +modextrapaths = {'PYTHONPATH': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['KMCLib/Backend'], +} + +sanity_check_commands = [ + "python -c 'from KMCLib import *'", + 'python %(builddir)s/%(name)s-%(version)s/python/unittest/utest.py' +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch new file mode 100644 index 00000000000..5649a5c63d2 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch @@ -0,0 +1,17 @@ +Relax test condition for test failing on PPC +See https://github.com/numpy/numpy/issues/15763 + +Author: Alexander Grund (TU Dresden) + +diff -aur numpy-1.16.2/numpy/core/tests/test_umath.py numpy-1.16.2-new/numpy/core/tests/test_umath.py +--- numpy-1.16.2/numpy/core/tests/test_umath.py 2021-03-29 12:29:48.950135026 +0200 ++++ numpy-1.16.2-new/numpy/core/tests/test_umath.py 2021-03-29 12:28:09.000000000 +0200 +@@ -2593,7 +2593,7 @@ + # are accurate down to a few epsilons. (Eg. on Linux 64-bit) + # So, give more leeway for long complex tests here: + # Can use 2.1 for > Ubuntu LTS Trusty (2014), glibc = 2.19. +- check(x_series, 50.0*eps) ++ check(x_series, 5e-19) + else: + check(x_series, 2.1*eps) + check(x_basic, 2.0*eps/1e-3) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..a3367b39bd9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,37 @@ +name = 'numpy' +version = '1.16.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_ZIP] +patches = [ # patches copied from SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb + 'numpy-1.16.2_relax-long-complex-test.patch', + 'numpy-1.16.6_add_flexiblas_detection.patch', + 'numpy-1.16.6_handle_failing_linalg_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', +] +checksums = [ + {'numpy-1.16.6.zip': 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff'}, + {'numpy-1.16.2_relax-long-complex-test.patch': '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb'}, + {'numpy-1.16.6_add_flexiblas_detection.patch': '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5'}, + {'numpy-1.16.6_handle_failing_linalg_test.patch': + 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, +] + +dependencies = [ + ('Python', '2.7.18'), + ('pytest', '4.6.11', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch new file mode 100644 index 00000000000..02528b44bc3 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch @@ -0,0 +1,181 @@ +Add flexiblas detection to numpy. +This is just a copy of the openblas detection with name changed. + +Åke Sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/distutils/system_info.py numpy-1.16.6/numpy/distutils/system_info.py +--- numpy-1.16.6.orig/numpy/distutils/system_info.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/distutils/system_info.py 2022-01-13 16:48:14.754235308 +0100 +@@ -20,6 +20,7 @@ + blas_info + lapack_info + openblas_info ++ flexiblas_info + blis_info + blas_opt_info # usage recommended + lapack_opt_info # usage recommended +@@ -395,6 +396,9 @@ + # openblas with embedded lapack + 'openblas_lapack': openblas_lapack_info, # use blas_opt instead + 'openblas_clapack': openblas_clapack_info, # use blas_opt instead ++ 'flexiblas': flexiblas_info, # use blas_opt instead ++ 'flexiblas_lapack': flexiblas_lapack_info, # use blas_opt instead ++ 'flexiblas_clapack': flexiblas_clapack_info, # use blas_opt instead + 'blis': blis_info, # use blas_opt instead + 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead + 'blas_mkl': blas_mkl_info, # use blas_opt instead +@@ -1549,6 +1553,16 @@ + self.set_info(**lapack_mkl_info) + return + ++ flexiblas_info = get_info('flexiblas_lapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ ++ flexiblas_info = get_info('flexiblas_clapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas_lapack') + if openblas_info: + self.set_info(**openblas_info) +@@ -1633,6 +1647,11 @@ + self.set_info(**blis_info) + return + ++ flexiblas_info = get_info('flexiblas') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas') + if openblas_info: + self.set_info(**openblas_info) +@@ -1749,6 +1768,126 @@ + return res + + ++class flexiblas_info(blas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ return True ++ ++ def calc_info(self): ++ c = customized_ccompiler() ++ ++ lib_dirs = self.get_lib_dirs() ++ ++ flexiblas_libs = self.get_libs('libraries', self._lib_names) ++ if flexiblas_libs == self._lib_names: # backward compat with 1.8.0 ++ flexiblas_libs = self.get_libs('flexiblas_libs', self._lib_names) ++ ++ info = self.check_libs(lib_dirs, flexiblas_libs, []) ++ ++ if c.compiler_type == "msvc" and info is None: ++ from numpy.distutils.fcompiler import new_fcompiler ++ f = new_fcompiler(c_compiler=c) ++ if f and f.compiler_type == 'gnu95': ++ # Try gfortran-compatible library files ++ info = self.check_msvc_gfortran_libs(lib_dirs, flexiblas_libs) ++ # Skip lapack check, we'd need build_ext to do it ++ assume_lapack = True ++ elif info: ++ assume_lapack = False ++ info['language'] = 'c' ++ ++ if info is None: ++ return ++ ++ # Add extra info for OpenBLAS ++ extra_info = self.calc_extra_info() ++ dict_append(info, **extra_info) ++ ++ if not (assume_lapack or self.check_embedded_lapack(info)): ++ return ++ ++ info['define_macros'] = [('HAVE_CBLAS', None)] ++ self.set_info(**info) ++ ++ def check_msvc_gfortran_libs(self, library_dirs, libraries): ++ # First, find the full path to each library directory ++ library_paths = [] ++ for library in libraries: ++ for library_dir in library_dirs: ++ # MinGW static ext will be .a ++ fullpath = os.path.join(library_dir, library + '.a') ++ if os.path.isfile(fullpath): ++ library_paths.append(fullpath) ++ break ++ else: ++ return None ++ ++ # Generate numpy.distutils virtual static library file ++ tmpdir = os.path.join(os.getcwd(), 'build', 'flexiblas') ++ if not os.path.isdir(tmpdir): ++ os.makedirs(tmpdir) ++ ++ info = {'library_dirs': [tmpdir], ++ 'libraries': ['flexiblas'], ++ 'language': 'f77'} ++ ++ fake_lib_file = os.path.join(tmpdir, 'flexiblas.fobjects') ++ fake_clib_file = os.path.join(tmpdir, 'flexiblas.cobjects') ++ with open(fake_lib_file, 'w') as f: ++ f.write("\n".join(library_paths)) ++ with open(fake_clib_file, 'w') as f: ++ pass ++ ++ return info ++ ++class flexiblas_lapack_info(flexiblas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ res = False ++ c = customized_ccompiler() ++ ++ tmpdir = tempfile.mkdtemp() ++ s = """void zungqr_(); ++ int main(int argc, const char *argv[]) ++ { ++ zungqr_(); ++ return 0; ++ }""" ++ src = os.path.join(tmpdir, 'source.c') ++ out = os.path.join(tmpdir, 'a.out') ++ # Add the additional "extra" arguments ++ try: ++ extra_args = info['extra_link_args'] ++ except Exception: ++ extra_args = [] ++ if sys.version_info < (3, 5) and sys.version_info > (3, 0) and c.compiler_type == "msvc": ++ extra_args.append("/MANIFEST") ++ try: ++ with open(src, 'wt') as f: ++ f.write(s) ++ obj = c.compile([src], output_dir=tmpdir) ++ try: ++ c.link_executable(obj, out, libraries=info['libraries'], ++ library_dirs=info['library_dirs'], ++ extra_postargs=extra_args) ++ res = True ++ except distutils.ccompiler.LinkError: ++ res = False ++ finally: ++ shutil.rmtree(tmpdir) ++ return res ++ ++class flexiblas_clapack_info(flexiblas_lapack_info): ++ _lib_names = ['flexiblas', 'lapack'] ++ + class openblas_info(blas_info): + section = 'openblas' + dir_env_var = 'OPENBLAS' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch new file mode 100644 index 00000000000..d85fb475809 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch @@ -0,0 +1,17 @@ +linalg/test_nan is marked xfail in at least 1.21.3 +Do so here too since it fails with newer openblas/compiler versions. + +Åke sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py numpy-1.16.6/numpy/linalg/tests/test_linalg.py +--- numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/linalg/tests/test_linalg.py 2022-01-13 17:21:36.658857878 +0100 +@@ -740,6 +740,9 @@ + for A, p in itertools.product(As, p_neg): + linalg.cond(A, p) + ++ @pytest.mark.xfail(True, run=False, ++ reason="Platform/LAPACK-dependent failure, " ++ "see gh-18914") + def test_nan(self): + # nans should be passed through, not converted to infs + ps = [None, 1, -1, 2, -2, 'fro'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch b/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch new file mode 100644 index 00000000000..32b41061f06 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch @@ -0,0 +1,43 @@ +Using Fortran compilers which differ "too much" from GCC fails building NumPy with something like +> A valid Fortran version was not found in this string: [...] + +See https://github.com/easybuilders/easybuild-easyblocks/issues/2518 and https://github.com/numpy/numpy/pull/26502 + +Fix by converting the hard error into a warning as the issue would be handled later if required. +E.g. for building NumPy we don't need a Fortran compiler at all. + +Author: Alexander Grund (TU Dresden) + +diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py +index eac4cbb477..8a1043fe26 100644 +--- a/numpy/distutils/fcompiler/gnu.py ++++ b/numpy/distutils/fcompiler/gnu.py +@@ -8,6 +8,7 @@ import hashlib + import base64 + import subprocess + from subprocess import Popen, PIPE, STDOUT ++from distutils import log + from numpy.distutils.exec_command import filepath_from_subprocess_output + from numpy.distutils.fcompiler import FCompiler + from distutils.version import LooseVersion +@@ -69,9 +70,9 @@ class GnuFCompiler(FCompiler): + # from the version string + return ('gfortran', v) + +- # If still nothing, raise an error to make the problem easy to find. +- err = 'A valid Fortran version was not found in this string:\n' +- raise ValueError(err + version_string) ++ # If still nothing, warn to make the problem easy to find. ++ log.warn('A valid Fortran version was not found in this string:\n' ++ + version_string) + + def version_match(self, version_string): + v = self.gnu_version_match(version_string) +@@ -539,7 +540,6 @@ def _can_target(cmd, arch): + + + if __name__ == '__main__': +- from distutils import log + from numpy.distutils import customized_fcompiler + log.set_verbosity(2) + diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..3627c92e3d1 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.6.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [('Python', '2.7.18')] + +use_pip = True + +exts_list = [ + ('contextlib2', '0.6.0.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['3355078a159fbb44ee60ea80abd0d87b80b78c248643b49aa6d94673b413609b'], + }), + ('zipp', '1.2.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['e0d9e63797e483a30d27e09fffd308c59a700d365ec34e93cc100844168bf921'], + }), + ('importlib_metadata', '2.1.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['52e65a0856f9ba7ea8f2c4ced253fb6c88d1a8c352cb1e916cff4eb17d5a693d'], + }), + ('typing', '3.10.0.0', { + 'source_tmpl': SOURCE_PY2_WHL, + 'checksums': ['c7219ef20c5fbf413b4567092adfc46fa6203cb8454eda33c3fc1afe1398a308'], + }), + ('py', '1.11.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378'], + }), + ('attrs', '21.4.0', { + 'modulename': 'attr', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4'], + }), + ('pluggy', '0.13.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('more_itertools', '5.0.0', { + 'source_tmpl': SOURCE_PY2_WHL, + 'checksums': ['c0a5785b1109a6bd7fac76d6837fd1feca158e54e521ccd2ae8bfe393cc9d4fc'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['5266a0fd000452f1b3467d782f079a4343c63aaa119221fbdc4e39577489ca5b'], + }), + ('six', '1.16.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254'], + }), + ('funcsigs', '1.0.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['330cc27ccbf7f1e992e69fef78261dc7c6569012cf397db8d3de0234e6c937ca'], + }), + ('configparser', '4.0.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['254c1d9c79f60c45dfde850850883d5aaa7f19a23f13561243a050d5a7c3fe4c'], + }), + ('packaging', '20.9', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['67714da7f7bc052e064859c05c595155bd1ee9f69f76557e21f051443c20947a'], + }), + (name, version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['a00a7d79cbbdfa9d21e7d0298392a8dd4123316bfac545075e6f8f24c94d8c97'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 3159e10b67763e41ffefe83e7d4968bc4fefec76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Sat, 5 Oct 2024 06:48:35 +0200 Subject: [PATCH 065/524] enable sanity pip check --- .../p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb index 3627c92e3d1..6d89384e9a0 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} dependencies = [('Python', '2.7.18')] use_pip = True +sanity_pip_check = True exts_list = [ ('contextlib2', '0.6.0.post1', { From 175e9afacf7679916d2306bd6c25f2a3ab21bedd Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 5 Oct 2024 10:45:03 +0200 Subject: [PATCH 066/524] add patch to SciPy-bundle 2024.05 that fixes test failure on aarch64 --- .../SciPy-bundle-2024.05-gfbf-2024a.eb | 3 ++ .../scipy-1.13.1_TestLinprogIPSparse.patch | 30 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb index 2abab977add..5584d888f30 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -64,12 +64,15 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.13.1_TestLinprogIPSparse.patch', ], 'checksums': [ {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.13.1_TestLinprogIPSparse.patch': + '7213c2690b76c69f7e7103529cea3fa2098c05fbea556f04325fab9ca8c065f5'}, ], }), ('numexpr', '2.10.0', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch new file mode 100644 index 00000000000..1b057319086 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch @@ -0,0 +1,30 @@ +disable problematic tests +TestLinprogIPSparse::test_bug_6139 + TestLinprogIPSparsePresolve::test_bug_6139 fail on Grace Hopper aarch64 +author: Sebastian Achilles (Juelich Supercomputing Centre) + +diff --git a/scipy/optimize/tests/test_linprog.py b/scipy/optimize/tests/test_linprog.py +index 49a0f8de5..8ffbb0b47 100644 +--- a/scipy/optimize/tests/test_linprog.py ++++ b/scipy/optimize/tests/test_linprog.py +@@ -1977,6 +1977,10 @@ if has_umfpack: + class TestLinprogIPSparse(LinprogIPTests): + options = {"sparse": True, "cholesky": False, "sym_pos": False} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") +@@ -2027,6 +2031,10 @@ class TestLinprogIPSparse(LinprogIPTests): + class TestLinprogIPSparsePresolve(LinprogIPTests): + options = {"sparse": True, "_sparse_presolve": True} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") From c8a586fd16997f1837376283c6d9991ff9b99a5b Mon Sep 17 00:00:00 2001 From: maximm Date: Sat, 5 Oct 2024 17:29:26 +0200 Subject: [PATCH 067/524] adding easyconfigs: ELPA-2024.05.001-foss-2024a.eb --- .../e/ELPA/ELPA-2024.05.001-foss-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb new file mode 100644 index 00000000000..c59f835b044 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb @@ -0,0 +1,46 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +# # + +name = 'ELPA' +version = '2024.05.001' +local_version = version.replace('.', '_') + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = "Eigenvalue SoLvers for Petaflop-Applications." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/%(namelower)s/%(namelower)s/-/archive/release_%(version)s/'] +sources = ['{}-release_{}.tar.gz'.format('%(namelower)s', local_version)] +patches = [ + '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', + '%(name)s-2023.05.001_fix_AVX512_support.patch', +] +checksums = [ + {'elpa-release_2024_05_001.tar.gz': '5e0c685536869bb91c230d70cac5e779ff418575681836f240b3e64e10b23f3e'}, + {'ELPA-2023.05.001_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'ELPA-2023.05.001_fix_AVX512_support.patch': 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('Python', '3.12.3'), + ('Perl', '5.38.2'), +] + +preconfigopts = './autogen.sh && export LDFLAGS="-lm $LDFLAGS" && autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + + +moduleclass = 'math' From 6a66242f05255654471da6432c8ab243b13c71d8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sat, 5 Oct 2024 17:46:55 +0200 Subject: [PATCH 068/524] Add Shapely and deps --- .../g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb | 32 +++++++++++++++++++ .../s/Shapely/Shapely-2.0.6-gfbf-2024a.eb | 28 ++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..74c03b228f7 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.13.0' + +homepage = 'https://trac.osgeo.org/geos' +description = "GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/%(namelower)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['47ec83ff334d672b9e4426695f15da6e6368244214971fabf386ff8ef6df39e4'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +# Build static and shared libraries +configopts = [ + '', + '-DBUILD_SHARED_LIBS=OFF', +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'lib/libgeos.so', 'lib/libgeos.a', 'include/%(namelower)s.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb new file mode 100644 index 00000000000..ad01c7a3723 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '2.0.6' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['997f6159b1484059ec239cacaa53467fd8b5564dabe186cd84ac2944663b0bf6'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('Cython', '3.0.10'), + ('GEOS', '3.13.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' From 2f1d3467b09d71ca2c7c2caa241a94144f3a3cab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Sat, 5 Oct 2024 18:23:34 +0200 Subject: [PATCH 069/524] add missing dependencies --- .../pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb index 6d89384e9a0..de53858bde9 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb @@ -70,10 +70,22 @@ exts_list = [ 'source_tmpl': SOURCE_WHL, 'checksums': ['254c1d9c79f60c45dfde850850883d5aaa7f19a23f13561243a050d5a7c3fe4c'], }), + ('pyparsing', '2.4.7', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b'], + }), ('packaging', '20.9', { 'source_tmpl': SOURCE_WHL, 'checksums': ['67714da7f7bc052e064859c05c595155bd1ee9f69f76557e21f051443c20947a'], }), + ('backports.functools_lru_cache', '1.6.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['77e27d0ffbb463904bdd5ef8b44363f6cd5ef503e664b3f599a3bf5843ed37cf'], + }), + ('wcwidth', '0.2.13', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859'], + }), (name, version, { 'source_tmpl': SOURCE_WHL, 'checksums': ['a00a7d79cbbdfa9d21e7d0298392a8dd4123316bfac545075e6f8f24c94d8c97'], From fa639e1ee4076f9837834212790f68157929897f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sat, 5 Oct 2024 20:25:36 +0200 Subject: [PATCH 070/524] Add HPX and dependencies --- .../gperftools-2.16-GCCcore-13.3.0.eb | 37 ++++++++++++++++ .../h/HDF5/HDF5-1.14.5-gompi-2024a.eb | 27 ++++++++++++ .../h/HPX/HPX-1.10.0-foss-2024a.eb | 44 +++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b142fbdb34d --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.16' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['737be182b4e42f5c7f595da2a7aa59ce0489a73d336d0d16847f2aa52d5221b4'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] +dependencies = [ + ('libunwind', '1.8.1'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +github_account = '%(name)s' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.so', 'lib/libtcmalloc.a', 'lib/libtcmalloc.so'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb new file mode 100644 index 00000000000..59171962924 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/HDFGroup/hdf5/archive'] +sources = ['hdf5_%(version)s.tar.gz'] +checksums = ['c83996dc79080a34e7b5244a1d5ea076abfd642ec12d7c25388e2fdd81d26350'] + +dependencies = [ + ('zlib', '1.3.1'), + ('Szip', '2.1.1'), +] + +postinstallcmds = [ + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5c++', + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5pcc', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb new file mode 100644 index 00000000000..493d4a7743f --- /dev/null +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -0,0 +1,44 @@ +# # +# Author: Benjamin Czaja (benjamin.czaja@surf.nl) +# Institute: SURF(sara) +# +# # +easyblock = 'CMakeMake' + +name = 'HPX' +version = '1.10.0' + +homepage = 'http://stellar-group.org/libraries/hpx/' +description = """HPX (High Performance ParalleX) is a general purpose C++ runtime system + for parallel and distributed applications of any scale.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/STEllAR-GROUP/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('Boost', '1.85.0'), + ('hwloc', '2.10.0'), + ('gperftools', '2.12'), +] + +configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " + +bin_lib_subdirs = ['lib/%(namelower)s/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'], +} + +modextrapaths = {'LD_LIBRARY_PATH': ['lib/%(namelower)s']} + +moduleclass = 'math' From b1fd4aeb24bba81c783102be9d1941c55527a4f4 Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Mon, 7 Oct 2024 04:49:53 +0100 Subject: [PATCH 071/524] adding easyconfigs: UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb --- ...C-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb new file mode 100644 index 00000000000..dc0b38a7c5b --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', +] +checksums = [ + {'v1.2.0.tar.gz': 'c1552797600835c0cf401b82dc89c4d27d5717f4fb805d41daca8e19f65e509d'}, + {'UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch': + '84157be5eae96d2501df076bcf0598b104adf80abeca028a144c4fb098638207'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'), + ('NCCL', '2.20.5', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +cuda_compute_capabilities = ['8.0', '8.9'] + +moduleclass = 'lib' From 46141a3f40e699433fac03af2d3ed81bd5a62da7 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Mon, 7 Oct 2024 09:27:53 +0530 Subject: [PATCH 072/524] Update UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb --- .../u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb index dc0b38a7c5b..ae39e3c18e8 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -50,6 +50,4 @@ sanity_check_commands = ["ucc_info -c"] modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} -cuda_compute_capabilities = ['8.0', '8.9'] - moduleclass = 'lib' From e8333ac953eec9be766778d3d16f9339806fe53a Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 7 Oct 2024 09:49:55 +0200 Subject: [PATCH 073/524] Set Cython as a builddependency --- easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb index ad01c7a3723..6e0094044ab 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb @@ -14,10 +14,13 @@ toolchain = {'name': 'gfbf', 'version': '2024a'} sources = [SOURCELOWER_TAR_GZ] checksums = ['997f6159b1484059ec239cacaa53467fd8b5564dabe186cd84ac2944663b0bf6'] +builddependencies = [ + ('Cython', '3.0.10'), +] + dependencies = [ ('Python', '3.12.3'), ('SciPy-bundle', '2024.05'), - ('Cython', '3.0.10'), ('GEOS', '3.13.0'), ] From 56f917f5986da6cfd0a51be88818dd81afdea631 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Oct 2024 11:15:58 +0200 Subject: [PATCH 074/524] adding easyconfigs: cmcrameri-1.9-gfbf-2023a.eb --- .../c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb b/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb new file mode 100644 index 00000000000..81e043144e9 --- /dev/null +++ b/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'cmcrameri' +version = '1.9' + +homepage = 'https://github.com/callumrollo/cmcrameri' +description = "Python wrapper around Fabio Crameri's perceptually uniform colormaps." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['56faf9b7f53eb03fed450137bec7dc25c1854929d7b841b9c75616fc2c357640'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 87592730f9652a319b2b2342b924491b58d64a63 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 7 Oct 2024 11:35:05 +0200 Subject: [PATCH 075/524] Added a configopt to zsh --- easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb index 2ddb0b4f403..2f5aa6a9ca5 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb @@ -15,6 +15,8 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] +configopts = '--without-tcsetpgrp' + builddependencies = [ ('binutils', '2.42'), ] From 5940aaa3f71624f9ea6a198ddda0318c0907c344 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 7 Oct 2024 12:22:57 +0200 Subject: [PATCH 076/524] adding easyconfigs: EVidenceModeler-2.1.0-foss-2023a.eb, FASTA-36.3.8i-GCC-12.3.0.eb, GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb, PASA-2.5.3-foss-2023a.eb, pblat-2.5.1-foss-2023a.eb --- .../EVidenceModeler-2.1.0-foss-2023a.eb | 41 ++++++++++++++ .../f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb | 36 +++++++++++++ .../GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb | 47 ++++++++++++++++ .../p/PASA/PASA-2.5.3-foss-2023a.eb | 53 +++++++++++++++++++ .../p/pblat/pblat-2.5.1-foss-2023a.eb | 41 ++++++++++++++ 5 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb new file mode 100644 index 00000000000..2e2ddf1dc83 --- /dev/null +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'EVidenceModeler' +version = '2.1.0' + +homepage = 'https://github.com/EVidenceModeler/EVidenceModeler' +description = """ EVM provides a flexible and intuitive framework for +combining diverse evidence types into a single automated gene structure annotation system.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/EVidenceModeler', + 'repo_name': '%(name)s', + 'tag': '%(name)s-v%(version)s', + 'recursive': True, + } +}] +checksums = ['0c6fbcc4897573ec24ee4e0c60a0a6fa3e20f7f4db513e89689a1638a0a6cd1d'] + +dependencies = [ + ('PASA', '2.5.3',), +] + +# Install ParaFly +postinstallcmds = ["cd %(installdir)s && make"] + +sanity_check_paths = { + 'files': ['EVidenceModeler'], + 'dirs': ['plugins/ParaFly', 'testing'], +} + +modextrapaths = { + 'EVM_HOME': '', +} + +sanity_check_commands = ['$EVM_HOME/EVidenceModeler --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb new file mode 100644 index 00000000000..58fd687455a --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = "FASTA" +version = "36.3.8i" +local_version_date = '14-Nov-2020' + +homepage = 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + +sanity_check_paths = { + 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] +} + +sanity_check_commands = ["fasta --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb new file mode 100644 index 00000000000..d391251a5a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2024-09-18' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb new file mode 100644 index 00000000000..3d3f419c8ff --- /dev/null +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'PASA' +version = '2.5.3' + +homepage = 'https://github.com/PASApipeline/PASApipeline' +description = """PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), + is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript + sequences to automatically model gene structures, and to maintain gene structure annotation consistent + with the most recently available experimental sequence data. PASA also identifies and classifies all + splicing variations supported by the transcript alignments.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/PASApipeline/PASApipeline/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] + +dependencies = [ + ('SQLite', '3.42.0'), + ('GMAP-GSNAP', '2024-09-18'), + ('pblat', '2.5.1'), + ('minimap2', '2.26'), + ('FASTA', '36.3.8i'), +] + +buildininstalldir = True + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' + +local_bins = [ + '%(namelower)s', + 'cdbfasta', + 'cdbyank', + 'cln2qual', + 'mdust', + 'psx', + 'seqclean', + 'seqclean.psx', + 'slclust', + 'trimpoly', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['command -v %(namelower)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb new file mode 100644 index 00000000000..a49d5fb0a74 --- /dev/null +++ b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'pblat' +version = '2.5.1' + +homepage = 'https://github.com/icebert/pblat' +description = """When the query file format is fasta, you can specify many threads to process it. + It can reduce run time linearly, and use almost equal memory as the original blat program. + This is useful when you blat a big query file to a huge reference like human whole genome sequence.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'icebert' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e85a4d752b8e159502d529f0f9e47579851a6b466b6c2f1f4d49f598642bc615'] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# use HTSlib dependency provided through EasyBuild +prebuildopts = "sed -i '5s/.\\/htslib/$\\{EBROOTHTSLIB\\}\\/include\\/htslib/' Makefile && " +prebuildopts += "sed -i '40s/ htslib\\/libhts.a//' Makefile && " +prebuildopts += "sed -i '41s/htslib\\/libhts.a/-lhts -lcurl/' Makefile && " +prebuildopts += "sed -i -e '/htslib\\/libhts.a:/,+2d' Makefile && " + +files_to_copy = [ + (['%(name)s'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["command -v %(name)s"] + +moduleclass = 'bio' From 2f81b66fe30db90a2736dcaf446cbdbf2a259131 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 12:35:31 +0200 Subject: [PATCH 077/524] Add HPX --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 493d4a7743f..301f804cc82 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -3,7 +3,7 @@ # Institute: SURF(sara) # # # -easyblock = 'CMakeMake' +easyblock = 'CMakeNinja' name = 'HPX' version = '1.10.0' @@ -27,7 +27,7 @@ dependencies = [ ('HDF5', '1.14.5'), ('Boost', '1.85.0'), ('hwloc', '2.10.0'), - ('gperftools', '2.12'), + ('gperftools', '2.16'), ] configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " From a06dbe8bb1f34fe17ae2b3ca16ce2540f9873cf5 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Oct 2024 12:51:14 +0200 Subject: [PATCH 078/524] adding easyconfigs: p7zip-17.05-GCCcore-13.3.0.eb --- .../p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..990ec0677d4 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.05' + +homepage = 'https://github.com/p7zip-project/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d2788f892571058c08d27095c22154579dfefb807ebe357d145ab2ddddefb1a6'] + +builddependencies = [ + ('binutils', '2.42'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +github_account = '%(name)s-project' +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + """echo '#!/bin/sh +%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z""", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), +] # 7z requires 7z.so plugin in same directory + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + "7z --help", + "7z x || test $? -gt 0", + """! 7z i | grep -q "Can't load" """, +] + +moduleclass = 'tools' From 3ec9888fd8859c074603d66885f75db96e34fbc1 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 7 Oct 2024 13:01:54 +0200 Subject: [PATCH 079/524] add checksum and remove empty patches from GMAP --- .../g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb index d391251a5a1..0a6c4bbf500 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['http://research-pub.gene.com/gmap/src/'] sources = [SOURCELOWER_TAR_GZ] -patches = [] +checksums = ['00d28c1a8c95295c8edd006cc0d1b5154cabe185de1f5a5dd8ccdb01fab38a18'] # with these deps you can use standard compressed files # details in http://research-pub.gene.com/gmap/src/README From 085e15c0b615abbad0c373c0cf5ffad8f06acda1 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Oct 2024 13:05:36 +0200 Subject: [PATCH 080/524] adding easyconfigs: likwid-5.3.0-GCC-13.3.0.eb --- .../l/likwid/likwid-5.3.0-GCC-13.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..a23dea7326c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.3.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] + +builddependencies = [ + ('Perl', '5.38.2'), +] +dependencies = [ + ('hwloc', '2.10.0'), +] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = "sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && " +prebuildopts += "sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' make/include_GCC.mk " +prebuildopts += "&& " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' +buildopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +installopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' +installopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' +installopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +installopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' +installopts += 'INSTALL_CHOWN="" ' + +maxparallel = 1 + +skipsteps = ['configure'] + +sanity_check_paths = { + 'files': ['bin/%(name)s-memsweeper', 'bin/%(name)s-mpirun', 'bin/%(name)s-perfctr', 'bin/%(name)s-perfscope', + 'bin/%(name)s-pin', 'bin/%(name)s-powermeter', 'bin/%(name)s-topology', 'lib/liblikwidpin.so', + 'lib/liblikwid.so', 'include/%(name)s.mod'], + 'dirs': ['man/man1'], +} + +moduleclass = 'tools' From c866a978fb0a1f85ea6e9420e8600e8a3cb069e5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 13:14:45 +0200 Subject: [PATCH 081/524] Add Qt6 and deps --- .../a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb | 36 ++++++++ .../double-conversion-3.3.0-GCCcore-13.3.0.eb | 37 ++++++++ .../n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb | 30 +++++++ .../n/NSS/NSS-3.104-GCCcore-13.3.0.eb | 61 +++++++++++++ .../q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb | 85 +++++++++++++++++++ .../Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch | 53 ++++++++++++ .../r/re2c/re2c-3.1-GCCcore-13.3.0.eb | 33 +++++++ .../s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb | 38 +++++++++ 8 files changed, 373 insertions(+) create mode 100644 easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5df6263ae2c --- /dev/null +++ b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# Authors:: Richard Lawrence - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'assimp' +version = '5.4.3' + +homepage = 'https://github.com/assimp/assimp' +description = """ + Open Asset Import Library (assimp) is a library to import and export various + 3d-model-formats including scene-post-processing to generate missing render data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['66dfbaee288f2bc43172440a55d0235dfc7bf885dda6435c038e8000e79582cb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('zlib', '1.3.1'), +] + +# workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315 +configopts = "-DASSIMP_WARNINGS_AS_ERRORS=OFF " + + +sanity_check_paths = { + 'files': ['include/%(name)s/types.h', 'lib/libassimp.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0b53c10d5f5 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ + +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.3.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + "-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a", + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/%(name)s/bignum.h', 'include/%(name)s/cached-powers.h', 'include/%(name)s/diy-fp.h', + 'include/%(name)s/%(name)s.h', 'include/%(name)s/fast-dtoa.h', 'include/%(name)s/fixed-dtoa.h', + 'include/%(name)s/ieee.h', 'include/%(name)s/strtod.h', 'include/%(name)s/utils.h', + 'lib/libdouble-conversion.a', 'lib/libdouble-conversion.so', 'lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6d16a7c419d --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/%(namelower)s/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%(version_major)s.so', 'lib/libplc%(version_major)s.a', 'lib/libplc%(version_major)s.so', 'lib/libplds%(version_major)s.a', 'lib/libplds%(version_major)s.so', 'lib/pkgconfig/%(namelower)s.pc'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..581af350164 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.104' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-3.39_pkgconfig.patch', + '%(name)s-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.104.tar.gz': 'e2763223622d1e76b98a43030873856f248af0a41b03b2fa2ca06a91bc50ac8e'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Perl', '5.38.2'), +] +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.3.1'), +] + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = 'NSS_ENABLE_WERROR=0 BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" OS_REL_CFLAGS="-D_XOPEN_SOURCE " && cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -' + +# building in parallel fails +parallel = 1 + +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = [ + '../dist/Linux*.OBJ/*', + (['../dist/public/*'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/%(namelower)s'], +} + +sanity_check_commands = [ + "multinit --help", + "%(namelower)s-config --version", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8c8888fe454 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb @@ -0,0 +1,85 @@ +easyblock = 'CMakeNinja' + +name = 'Qt6' +version = '6.7.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + '%(name)s-6.6.3_fix_OF-Gentoo.patch', + 'Qt6-6.7.2_fix_cpu_features.patch', +] +checksums = [ + {'qt-everywhere-src-6.7.2.tar.xz': '0aaea247db870193c260e8453ae692ca12abc1bd841faa1a6e6c99459968ca8a'}, + {'Qt6-6.6.3_fix_OF-Gentoo.patch': 'd4d4878ac76cb985e45eb3b6e90ba2233f65807d6bd9bbe2b71365b181347b7b'}, + {'Qt6-6.7.2_fix_cpu_features.patch': 'faaa2268fca9d59fa8f25cbe6cf4a46baa29669f1fecbc1968ddd111c117a101'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('re2c', '3.1'), +] +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.80.4'), + ('PCRE2', '10.43'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('libwebp', '1.4.0'), + ('JasPer', '4.2.4'), + ('HarfBuzz', '9.0.0'), + ('SQLite', '3.45.3'), + ('graphite2', '1.3.14'), + ('assimp', '5.4.3'), # for Qt 3D + ('FFmpeg', '7.0.2'), + ('X11', '20240607'), + ('fontconfig', '2.15.0'), + ('zlib', '1.3.1'), + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('freetype', '2.13.2'), # WebEngine + ('DBus', '1.15.8'), + ('libevent', '2.1.12'), # WebEngine + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '3.0.1'), # WebEngine + ('NSS', '3.104'), # WebEngine, required + ('snappy', '1.2.1'), # WebEngine + ('OpenSSL', '3', '', SYSTEM), + ('ICU', '75.1'), + ('nodejs', '20.13.1'), + # ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf +] + +preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ../qt-everywhere-src-%(version)s/qtwebengine/src/gn/CMakeLists.txt &&' # Typo +configopts = "-Wno-dev -DFEATURE_qtpdf_build=OFF -DQT_AVOID_CMAKE_ARCHIVING_API=ON -DPython3_ROOT_DIR=$EBROOTPYTHON -DBUILD_qtwayland=OFF " + + +# Removed from Qt6.0.0 but may be added back in the future +# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 + +sanity_check_paths = { + 'files': ['bin/qmake6', 'lib/libQt6Core.so', 'lib/libQt6WebEngineCore.so'], + 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], +} + +sanity_check_commands = ['qmake6 --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch new file mode 100644 index 00000000000..e8dd6232e68 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch @@ -0,0 +1,53 @@ +# What: Comment out incorrect detection of CPU features when AVX2 flag is set +# Author: maxim-masterov (SURF) +diff -Nru qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h qt-everywhere-src-6.7.2/qtbase/src/corelib/global/qsimd_p.h +--- qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h 2024-09-20 12:05:26.732359000 +0200 ++++ qt-everywhere-src-6.7.2/qtbase/src/corelib/global/qsimd_p.h 2024-09-23 22:31:44.861936347 +0200 +@@ -227,14 +227,14 @@ + # if defined(__AVX2__) + // List of features present with -march=x86-64-v3 and not architecturally + // implied by __AVX2__ +-# define ARCH_HASWELL_MACROS \ +- (__AVX2__ + __BMI__ + __BMI2__ + __F16C__ + __FMA__ + __LZCNT__ + __POPCNT__) +-# if ARCH_HASWELL_MACROS != 7 +-# error "Please enable all x86-64-v3 extensions; you probably want to use -march=haswell or -march=x86-64-v3 instead of -mavx2" +-# endif +-static_assert(ARCH_HASWELL_MACROS, "Undeclared identifiers indicate which features are missing."); +-# define __haswell__ 1 +-# undef ARCH_HASWELL_MACROS ++//# define ARCH_HASWELL_MACROS \ ++// (__AVX2__ + __BMI__ + __BMI2__ + __F16C__ + __FMA__ + __LZCNT__ + __POPCNT__) ++//# if ARCH_HASWELL_MACROS != 7 ++//# error "Please enable all x86-64-v3 extensions; you probably want to use -march=haswell or -march=x86-64-v3 instead of -mavx2" ++//# endif ++//static_assert(ARCH_HASWELL_MACROS, "Undeclared identifiers indicate which features are missing."); ++//# define __haswell__ 1 ++//# undef ARCH_HASWELL_MACROS + # endif + + // x86-64 sub-architecture version 4 +@@ -244,15 +244,15 @@ + // with AVX512 support and it includes all of these too. The GNU libc subdir for + // this is "glibc-hwcaps/x86-64-v4". + // +-# define ARCH_SKX_MACROS (__AVX512F__ + __AVX512BW__ + __AVX512CD__ + __AVX512DQ__ + __AVX512VL__) +-# if ARCH_SKX_MACROS != 0 +-# if ARCH_SKX_MACROS != 5 +-# error "Please enable all x86-64-v4 extensions; you probably want to use -march=skylake-avx512 or -march=x86-64-v4 instead of -mavx512f" +-# endif +-static_assert(ARCH_SKX_MACROS, "Undeclared identifiers indicate which features are missing."); +-# define __skylake_avx512__ 1 +-# endif +-# undef ARCH_SKX_MACROS ++//# define ARCH_SKX_MACROS (__AVX512F__ + __AVX512BW__ + __AVX512CD__ + __AVX512DQ__ + __AVX512VL__) ++//# if ARCH_SKX_MACROS != 0 ++//# if ARCH_SKX_MACROS != 5 ++//# error "Please enable all x86-64-v4 extensions; you probably want to use -march=skylake-avx512 or -march=x86-64-v4 instead of -mavx512f" ++//# endif ++//static_assert(ARCH_SKX_MACROS, "Undeclared identifiers indicate which features are missing."); ++//# define __skylake_avx512__ 1 ++//# endif ++//# undef ARCH_SKX_MACROS + #endif /* Q_PROCESSOR_X86 */ + + // NEON intrinsics diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d40fa786722 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.1' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/skvadrik/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +configopts = '--disable-rust' + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..aaa018251cc --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.2.1' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-1.1.9_use-default-rtti.patch'] +checksums = [ + {'1.2.1.tar.gz': '736aeb64d86566d2236ddffa2865ee5d7a82d26c9016b36218fcc27ea4f09f86'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = [ + "-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF", + "-DBUILD_SHARED_LIBS=ON -DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF", +] + + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.so', 'include/%(name)s.h'], + 'dirs': [], +} + +moduleclass = 'lib' From 4045bd50eefd8e4a90f30110f57933d94f175e87 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 13:18:18 +0200 Subject: [PATCH 082/524] Add comments to the patch --- easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb | 2 +- .../easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb index 8c8888fe454..be461945080 100644 --- a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb @@ -23,7 +23,7 @@ patches = [ checksums = [ {'qt-everywhere-src-6.7.2.tar.xz': '0aaea247db870193c260e8453ae692ca12abc1bd841faa1a6e6c99459968ca8a'}, {'Qt6-6.6.3_fix_OF-Gentoo.patch': 'd4d4878ac76cb985e45eb3b6e90ba2233f65807d6bd9bbe2b71365b181347b7b'}, - {'Qt6-6.7.2_fix_cpu_features.patch': 'faaa2268fca9d59fa8f25cbe6cf4a46baa29669f1fecbc1968ddd111c117a101'}, + {'Qt6-6.7.2_fix_cpu_features.patch': '3f37e7a4e4ed38cc82037be9504bc644e48bf258555ffff848183142725c9dc8'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch index e8dd6232e68..0109ba0726b 100644 --- a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch +++ b/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch @@ -1,4 +1,7 @@ -# What: Comment out incorrect detection of CPU features when AVX2 flag is set +# What: Comment out incorrect detection of CPU features when only AVX2 flag is set. +# See relevant bug reports: +# https://bugs.gentoo.org/908420 +# https://bugs.gentoo.org/898644 # Author: maxim-masterov (SURF) diff -Nru qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h qt-everywhere-src-6.7.2/qtbase/src/corelib/global/qsimd_p.h --- qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h 2024-09-20 12:05:26.732359000 +0200 From 93c7e4bc55aebdb6cc8deb6abc2757ddfcb002ec Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 13:26:47 +0200 Subject: [PATCH 083/524] Move Qt files to the right place --- easybuild/easyconfigs/q/Qt6/{tmp => }/Qt6-6.7.2-GCCcore-13.3.0.eb | 0 .../easyconfigs/q/Qt6/{tmp => }/Qt6-6.7.2_fix_cpu_features.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/Qt6/{tmp => }/Qt6-6.7.2-GCCcore-13.3.0.eb (100%) rename easybuild/easyconfigs/q/Qt6/{tmp => }/Qt6-6.7.2_fix_cpu_features.patch (100%) diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb similarity index 100% rename from easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2-GCCcore-13.3.0.eb rename to easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2_fix_cpu_features.patch similarity index 100% rename from easybuild/easyconfigs/q/Qt6/tmp/Qt6-6.7.2_fix_cpu_features.patch rename to easybuild/easyconfigs/q/Qt6/Qt6-6.7.2_fix_cpu_features.patch From 5f68ab7662a6cbc389e728429d27a29f2b6578e2 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Oct 2024 13:35:19 +0200 Subject: [PATCH 084/524] adding easyconfigs: tbb-2021.13.0-GCCcore-13.3.0.eb --- .../t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c8b2b71819c --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.13.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +# The following option is needed to supress the "stringop-overflow error". +# See https://github.com/oneapi-src/oneTBB/issues/1180#issuecomment-1690958371 for details. +toolchainopts = {'extra_cxxflags': '-Wno-error=stringop-overflow'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ad5dd08954b39d113dc5b3f8a8dc6dc1fd5250032b7c491eb07aed5c94133e1'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('hwloc', '2.10.0'), +] + + +sanity_check_paths = { + 'files': ['lib/libtbb.so', 'lib/libtbbmalloc.so'], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' From 260474271455660b3bcf5b081914b4290f247302 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 7 Oct 2024 14:18:10 +0200 Subject: [PATCH 085/524] Added toolchainopts and configopts to GEOS --- easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb index f409af68e96..839a0000216 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb @@ -7,6 +7,7 @@ homepage = 'https://trac.osgeo.org/geos' description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} source_urls = ['https://download.osgeo.org/geos/'] sources = [SOURCELOWER_TAR_BZ2] @@ -14,6 +15,9 @@ checksums = ['34c7770bf0090ee88488af98767d08e779f124fa33437e0aabec8abd4609fec6'] builddependencies = [('CMake', '3.29.3')] +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + sanity_check_paths = { 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos_c.so', 'include/geos.h'], 'dirs': [], From 663fdda31a2b076bfe7c76b3ba91f45049c25eff Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 14:21:41 +0200 Subject: [PATCH 086/524] Fix style issues --- easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb | 4 +++- easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb | 7 +++++-- easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb | 9 +++++++-- 3 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb index 6d16a7c419d..8d1341af57b 100644 --- a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb @@ -21,7 +21,9 @@ configopts = "--disable-debug --enable-optimize --enable-64bit" sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%(version_major)s.so', 'lib/libplc%(version_major)s.a', 'lib/libplc%(version_major)s.so', 'lib/libplds%(version_major)s.a', 'lib/libplds%(version_major)s.so', 'lib/pkgconfig/%(namelower)s.pc'], + 'files': ['bin/%(namelower)s-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%(version_major)s.so', + 'lib/libplc%(version_major)s.a', 'lib/libplc%(version_major)s.so', 'lib/libplds%(version_major)s.a', + 'lib/libplds%(version_major)s.so', 'lib/pkgconfig/%(namelower)s.pc'], 'dirs': ['include/%(namelower)s'], } diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb index 581af350164..fb301be49d5 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb @@ -33,13 +33,16 @@ dependencies = [ # disable use of -Werror to work around compilation errors with newer glibc versions, # see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 -buildopts = 'NSS_ENABLE_WERROR=0 BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" OS_REL_CFLAGS="-D_XOPEN_SOURCE " && cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -' +buildopts = 'NSS_ENABLE_WERROR=0 BUILD_OPT=1 USE_64=1 ' +buildopts += 'CPATH="$EBROOTNSPR/include/nspr:$CPATH" OS_REL_CFLAGS="-D_XOPEN_SOURCE "' +buildopts += ' && cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -' # building in parallel fails parallel = 1 # optional testsuite (takes a long time) -# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && " +# buildopts += " BUILD_OPT=1 USE_64=1 ./all.sh " files_to_copy = [ '../dist/Linux*.OBJ/*', diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb index be461945080..dd8446f91c4 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb @@ -68,8 +68,13 @@ dependencies = [ # ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf ] -preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ../qt-everywhere-src-%(version)s/qtwebengine/src/gn/CMakeLists.txt &&' # Typo -configopts = "-Wno-dev -DFEATURE_qtpdf_build=OFF -DQT_AVOID_CMAKE_ARCHIVING_API=ON -DPython3_ROOT_DIR=$EBROOTPYTHON -DBUILD_qtwayland=OFF " +preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt && ' + +preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' +preconfigopts += '../qt-everywhere-src-%(version)s/qtwebengine/src/gn/CMakeLists.txt && ' # Typo + +configopts = "-Wno-dev -DFEATURE_qtpdf_build=OFF -DQT_AVOID_CMAKE_ARCHIVING_API=ON " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON -DBUILD_qtwayland=OFF " # Removed from Qt6.0.0 but may be added back in the future From e1f99a49558f08ed848a598beb4a425aa06f4ebd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 17:03:14 +0200 Subject: [PATCH 087/524] Add netCDF for 2024a --- .../netCDF-C++4-4.3.1-gompi-2024a.eb | 28 ++++++++++ .../netCDF-Fortran-4.6.1-gompi-2024a.eb | 28 ++++++++++ .../n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 54 +++++++++++++++++++ .../netcdf4-python-1.7.1.post2-foss-2024a.eb | 54 +++++++++++++++++++ ...st2_relax_tolerance_compression_test.patch | 15 ++++++ .../p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb | 35 ++++++++++++ 6 files changed, 214 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..1b9a80b189c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [ + ('netCDF', '4.9.2'), +] + + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb new file mode 100644 index 00000000000..2bc6e207794 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb new file mode 100644 index 00000000000..2229ea87111 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -0,0 +1,54 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch'] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch': + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('CMake', '3.29.3'), + ('Doxygen', '1.11.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('cURL', '8.7.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.6'), + ('bzip2', '1.0.8'), + ('libxml2', '2.12.7'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb new file mode 100644 index 00000000000..a7958767777 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.7.1.post2' + + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = "Python/numpy interface to netCDF." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('netCDF', '4.9.2'), + ('cURL', '8.7.1'), + ('mpi4py', '4.0.0'), +] + +fix_python_shebang_for = ['bin/*'] +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cftime', '1.6.4', { + 'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netcdf4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'}, + {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch': + '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..be4deb77f96 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-1.7.1.post2.orig/test/test_compression_szip.py netcdf4-1.7.1.post2/test/test_compression_szip.py +--- netcdf4-1.7.1.post2.orig/test/test_compression_szip.py 2024-10-07 16:01:21.276893761 +0200 ++++ netcdf4-1.7.1.post2/test/test_compression_szip.py 2024-10-07 16:27:47.424436617 +0200 +@@ -35,7 +35,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb new file mode 100644 index 00000000000..b586cfd0da4 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.13.0' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Perl', '5.38.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = [ + '', + '--enable-shared', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = {'PNETCDF': ''} + +moduleclass = 'data' From 1a89001e6563db37831be579d76cb10691e101b3 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 17:08:19 +0200 Subject: [PATCH 088/524] Revert "Add netCDF for 2024a" This reverts commit e1f99a49558f08ed848a598beb4a425aa06f4ebd. --- .../netCDF-C++4-4.3.1-gompi-2024a.eb | 28 ---------- .../netCDF-Fortran-4.6.1-gompi-2024a.eb | 28 ---------- .../n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 54 ------------------- .../netcdf4-python-1.7.1.post2-foss-2024a.eb | 54 ------------------- ...st2_relax_tolerance_compression_test.patch | 15 ------ .../p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb | 35 ------------ 6 files changed, 214 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb delete mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb delete mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb delete mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch delete mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb deleted file mode 100644 index 1b9a80b189c..00000000000 --- a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'netCDF-C++4' -version = '4.3.1' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2024a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] - -dependencies = [ - ('netCDF', '4.9.2'), -] - - -sanity_check_paths = { - 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], - 'dirs': [], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb deleted file mode 100644 index 2bc6e207794..00000000000 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.6.1' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2024a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] - -builddependencies = [ - ('M4', '1.4.19'), -] -dependencies = [ - ('netCDF', '4.9.2'), - ('bzip2', '1.0.8'), -] - -# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -parallel = 1 - - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb deleted file mode 100644 index 2229ea87111..00000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb +++ /dev/null @@ -1,54 +0,0 @@ -name = 'netCDF' -version = '4.9.2' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2024a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/%(namelower)s-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch'] -checksums = [ - {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, - {'%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch': - '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, -] - -builddependencies = [ - ('Autotools', '20231222'), - ('CMake', '3.29.3'), - ('Doxygen', '1.11.0'), -] -dependencies = [ - ('HDF5', '1.14.5'), - ('cURL', '8.7.1'), - ('Szip', '2.1.1'), - ('zstd', '1.5.6'), - ('bzip2', '1.0.8'), - ('libxml2', '2.12.7'), -] - -# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso -# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 -# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 -preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" - " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") - -# make sure both static and shared libs are built -# and disable "remote" tests that access a unreliable external test server over internet -configopts = [ - "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", - "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", -] - -# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests -pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " -runtest = 'test' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb deleted file mode 100644 index a7958767777..00000000000 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'netcdf4-python' -version = '1.7.1.post2' - - -homepage = 'https://unidata.github.io/netcdf4-python/' -description = "Python/numpy interface to netCDF." - -toolchain = {'name': 'foss', 'version': '2024a'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.12.3'), - ('SciPy-bundle', '2024.05'), - ('netCDF', '4.9.2'), - ('cURL', '8.7.1'), - ('mpi4py', '4.0.0'), -] - -fix_python_shebang_for = ['bin/*'] -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('cftime', '1.6.4', { - 'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'], - }), - (name, version, { - 'patches': [ - 'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch', - ], - 'source_tmpl': 'netcdf4-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], - 'checksums': [ - {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'}, - {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch': - '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'}, - ], - }), -] - -sanity_check_paths = { - 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "nc4tonc3 --help", - "nc3tonc4 --help", - "ncinfo --help", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch deleted file mode 100644 index be4deb77f96..00000000000 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch +++ /dev/null @@ -1,15 +0,0 @@ -# Relax tolerance in the compression_szip test to avoid fails on some systems. -# author: maxim-masterov (SURF) -# -diff -Nru netcdf4-1.7.1.post2.orig/test/test_compression_szip.py netcdf4-1.7.1.post2/test/test_compression_szip.py ---- netcdf4-1.7.1.post2.orig/test/test_compression_szip.py 2024-10-07 16:01:21.276893761 +0200 -+++ netcdf4-1.7.1.post2/test/test_compression_szip.py 2024-10-07 16:27:47.424436617 +0200 -@@ -35,7 +35,7 @@ - assert_almost_equal(datarr,f.variables['data'][:]) - assert f.variables['data'].filters() ==\ - {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} -- assert_almost_equal(datarr,f.variables['data_szip'][:]) -+ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) - dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} - assert f.variables['data_szip'].filters() == dtest - f.close() diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb deleted file mode 100644 index b586cfd0da4..00000000000 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PnetCDF' -version = '1.13.0' - -homepage = 'https://parallel-netcdf.github.io/' -description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" - -toolchain = {'name': 'gompi', 'version': '2024a'} - -source_urls = ['https://parallel-netcdf.github.io/Release'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491'] - -builddependencies = [ - ('Autotools', '20231222'), - ('Perl', '5.38.2'), -] - -preconfigopts = "autoreconf -f -i && " -configopts = [ - '', - '--enable-shared', -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', - 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + - ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -modextrapaths = {'PNETCDF': ''} - -moduleclass = 'data' From 15ddd89ac8d83c24955bbd07fb8d3d3efbe7cd04 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 7 Oct 2024 21:41:35 +0200 Subject: [PATCH 089/524] Update easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb index 74c03b228f7..db9fbe7de2f 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb @@ -25,7 +25,7 @@ configopts = [ sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'lib/libgeos.so', 'lib/libgeos.a', 'include/%(namelower)s.h'], + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], 'dirs': [], } From 7711a2fcaed00d1e26b83be232c588952bfdf344 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 7 Oct 2024 21:41:40 +0200 Subject: [PATCH 090/524] Update easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb index db9fbe7de2f..11abbcb4252 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb @@ -9,7 +9,7 @@ description = "GEOS (Geometry Engine - Open Source) is a C++ port of the Java To toolchain = {'name': 'GCC', 'version': '13.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.osgeo.org/%(namelower)s/'] +source_urls = ['https://download.osgeo.org/geos/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['47ec83ff334d672b9e4426695f15da6e6368244214971fabf386ff8ef6df39e4'] From 2bfc0cbaa88cb096119076e35ba5634c4a03b885 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 8 Oct 2024 14:05:08 +0200 Subject: [PATCH 091/524] update the sanity check command --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index 2e2ddf1dc83..76537b0b48e 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -36,6 +36,6 @@ modextrapaths = { 'EVM_HOME': '', } -sanity_check_commands = ['$EVM_HOME/EVidenceModeler --help'] +sanity_check_commands = ['$EVM_HOME/EVidenceModeler --version'] moduleclass = 'bio' From da0628988bb511378969574892b28ff451eea42e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 8 Oct 2024 14:15:55 +0200 Subject: [PATCH 092/524] changes requested in PR --- .../KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb | 18 +++++++++--------- ... pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb} | 4 +++- 2 files changed, 12 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/p/pytest/{pytest-4.6.11-foss-2023a-Python-2.7.18.eb => pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb} (97%) diff --git a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb index 77d18cbdc50..96bbb5992bf 100644 --- a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb @@ -16,12 +16,12 @@ checksums = ['796620a67ad010df4b11734f703151c17441f82cef026f3d56386a34056d0213'] builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), ] dependencies = [ ('Python', '2.7.18'), ('numpy', '1.16.6', versionsuffix), - ('SWIG', '4.1.1'), ] start_dir = 'c++' @@ -31,10 +31,13 @@ preconfigopts += 'make CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" prebuildopts = 'export CPATH=$EBROOTPYTHON/include/python%(pyshortver)s:$CPATH && ' -postinstallcmds = [ - 'cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s"', - 'cp -r "%(builddir)s/../python/src/KMCLib/Backend/"* "%(installdir)s/KMCLib/Backend/"', -] +buildopts = ' && cd "%(builddir)s" && ' +buildopts += 'cp -r "../python/src/KMCLib/Backend/"* "%(name)s-%(version)s/python/src/KMCLib/Backend/"' + +test_cmd = 'export PYTHONPATH="%(builddir)s/%(name)s-%(version)s/python/src:$PYTHONPATH" && ' +test_cmd += 'python "%(builddir)s/%(name)s-%(version)s/python/unittest/utest.py"' + +postinstallcmds = ['cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s"'] modextrapaths = {'PYTHONPATH': ''} @@ -43,9 +46,6 @@ sanity_check_paths = { 'dirs': ['KMCLib/Backend'], } -sanity_check_commands = [ - "python -c 'from KMCLib import *'", - 'python %(builddir)s/%(name)s-%(version)s/python/unittest/utest.py' -] +sanity_check_commands = ["python -c 'from KMCLib import *'"] moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb similarity index 97% rename from easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb rename to easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb index de53858bde9..470efa5624e 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} dependencies = [('Python', '2.7.18')] @@ -97,4 +97,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ['pytest --help'] + moduleclass = 'tools' From 5637fe5bed2e0fa6a6a9fba6cd9cd208d832763c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 8 Oct 2024 15:35:20 +0200 Subject: [PATCH 093/524] update RPATH in NextPolish + patch patchelf-0.18.0 --- .../NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb | 93 +++++++++++++++++++ .../patchelf-0.18.0-GCCcore-12.3.0.eb | 6 +- .../patchelf-0.18.0_fix-alignment.patch | 31 +++++++ 3 files changed, 129 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..29930bc094a --- /dev/null +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb @@ -0,0 +1,93 @@ +easyblock = 'MakeCp' + +name = 'NextPolish' +version = '1.4.1' + +homepage = 'https://github.com/Nextomics/NextPolish' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] +sources = [{ + 'download_filename': 'v%(version)s/%(name)s.tgz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] + +builddependencies = [('patchelf', '0.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('BWA', '0.7.17'), + ('SAMtools', '1.18'), + ('minimap2', '2.26'), + ('bzip2', '1.0.8'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +# fix make -C util - warning: jobserver unavailable +parallel = 1 + +# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 +# + use SAMtools and minimap2 from EB +prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count/' Makefile && " +prebuildopts += "rm -rf util/bwa && rm -fr util/minimap2 && rm -rf util/samtools && " +prebuildopts += ( + "sed -i" + " -e 's/seq_split seq_count bwa_ samtools_ minimap2_/seq_split seq_count/'" + " -e '/BWADIR/d'" + " -e '/bwa_:/d'" + " -e '/SAMTOOLSDIR/d'" + " -e '/MINIMAP2DIR/d'" + " -e '/samtools_:/d'" + " -e '/minimap2_:/d'" + " util/Makefile && " +) +postinstallcmds = [ + # links to binaries + "cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa && " + "ln -s $EBROOTSAMTOOLS/bin/samtools && ln -s $EBROOTMINIMAP2/bin/minimap2", + # set RPATH to calgs.so + "patchelf --force-rpath --set-rpath '\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib' %(installdir)s/lib/calgs.so", + # set RPATH to nextpolish1.so and nextpolish2.so + "patchelf --force-rpath --set-rpath " + "'\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib' %(installdir)s/lib/nextpolish1.so", + "patchelf --force-rpath --set-rpath " + "'\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib' %(installdir)s/lib/nextpolish2.so", +] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] + +sanity_check_paths = { + 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa', 'bin/samtools'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'nextPolish --help', + 'nextPolish %(installdir)s/test_data/run.cfg' +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb index b87a53d6bda..d213a037191 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch new file mode 100644 index 00000000000..20a233ddc66 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch @@ -0,0 +1,31 @@ +Author - Pavel Tománek +Fix alignment problem when rewriting sections +https://github.com/NixOS/patchelf/pull/566 +--- src/patchelf.cc.orig 2024-10-07 16:45:17.515584318 +0200 ++++ src/patchelf.cc 2024-10-07 16:47:14.622270000 +0200 +@@ -843,7 +843,7 @@ + neededSpace += headerTableSpace; + debug("needed space is %d\n", neededSpace); + +- Elf_Off startOffset = roundUp(fileContents->size(), getPageSize()); ++ Elf_Off startOffset = roundUp(fileContents->size(), alignStartPage); + + // In older version of binutils (2.30), readelf would check if the dynamic + // section segment is strictly smaller than the file (and not same size). +@@ -879,7 +879,7 @@ + rdi(lastSeg.p_type) == PT_LOAD && + rdi(lastSeg.p_flags) == (PF_R | PF_W) && + rdi(lastSeg.p_align) == alignStartPage) { +- auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), getPageSize()); ++ auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), alignStartPage); + if (segEnd == startOffset) { + auto newSz = startOffset + neededSpace - rdi(lastSeg.p_offset); + wri(lastSeg.p_filesz, wri(lastSeg.p_memsz, newSz)); +@@ -898,6 +898,7 @@ + wri(phdr.p_filesz, wri(phdr.p_memsz, neededSpace)); + wri(phdr.p_flags, PF_R | PF_W); + wri(phdr.p_align, alignStartPage); ++ assert(startPage % alignStartPage == startOffset % alignStartPage); + } + + normalizeNoteSegments(); From 9daecde94f34ce7daec8bb729dffbe13b7619676 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 9 Oct 2024 09:43:19 +0200 Subject: [PATCH 094/524] fix installation --- .../k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb index 96bbb5992bf..12cf687bb00 100644 --- a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb @@ -31,13 +31,13 @@ preconfigopts += 'make CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" prebuildopts = 'export CPATH=$EBROOTPYTHON/include/python%(pyshortver)s:$CPATH && ' -buildopts = ' && cd "%(builddir)s" && ' -buildopts += 'cp -r "../python/src/KMCLib/Backend/"* "%(name)s-%(version)s/python/src/KMCLib/Backend/"' +buildopts = ' && cp wrap/Backend.py wrap/_Backend.so wrap/Custom.py wrap/_Custom.so' +buildopts += ' "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib/Backend/"' test_cmd = 'export PYTHONPATH="%(builddir)s/%(name)s-%(version)s/python/src:$PYTHONPATH" && ' test_cmd += 'python "%(builddir)s/%(name)s-%(version)s/python/unittest/utest.py"' -postinstallcmds = ['cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s"'] +install_cmd = 'cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s/"' modextrapaths = {'PYTHONPATH': ''} From 97bba67a06bb8e3f793f0136b0fcb11485923059 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 9 Oct 2024 12:35:49 +0200 Subject: [PATCH 095/524] update sanity check command --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index 76537b0b48e..a11cf7fed7c 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -36,6 +36,6 @@ modextrapaths = { 'EVM_HOME': '', } -sanity_check_commands = ['$EVM_HOME/EVidenceModeler --version'] +sanity_check_commands = ["$EVM_HOME/EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"] moduleclass = 'bio' From 9b12318bcff1749781d9eb71c23e21bc3a79ed01 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 9 Oct 2024 13:12:58 +0200 Subject: [PATCH 096/524] adding easyconfigs: waLBerla-6.1-foss-2023a.eb --- .../w/waLBerla/waLBerla-6.1-foss-2023a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb new file mode 100644 index 00000000000..85f6371e807 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb @@ -0,0 +1,56 @@ +# easyconfig file for waLBerla v6.1 +easyblock = 'CMakeMakeCp' + +name = 'waLBerla' +version = '6.1' + +homepage = "https://walberla.net/index.html" +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost.MPI', '1.82.0'), +] + +parallel = 1 + +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" + + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/*'], 'build'), + (['%(start_dir)s/src/*'], 'src'), +] + +sanity_check_paths = { + 'files': [ + 'build/src/waLBerlaDefinitions.h', + 'build/apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'build/utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'build/apps', 'build/tests', 'build/utilities'] +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/build/apps/tutorials/lbm %(builddir)s/", + "cd %(builddir)s/lbm && chmod -R u+w . && ./01_BasicLBM 01_BasicLBM.prm", +] + +moduleclass = 'chem' From b2295ce4b662851c3b387f945e4b5ac80cb00d42 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 9 Oct 2024 13:13:40 +0200 Subject: [PATCH 097/524] adding easyconfigs: waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb --- .../waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b77e1abbaca --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,63 @@ +# easyconfig file for waLBerla v6.1 +easyblock = 'CMakeMakeCp' + +name = 'waLBerla' +version = '6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://walberla.net/index.html" +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost.MPI', '1.82.0'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +parallel = 1 + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " +configopts += "-DCMAKE_CUDA_ARCHITECTURES='%(cuda_cc_cmake)s' " +configopts += "-DWALBERLA_BUILD_WITH_CUDA=ON " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" + + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/*'], 'build'), + (['%(start_dir)s/src/*'], 'src'), +] + +sanity_check_paths = { + 'files': [ + 'build/src/waLBerlaDefinitions.h', + 'build/apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'build/utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'build/apps', 'build/tests', 'build/utilities'] +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/build/apps/tutorials/lbm %(builddir)s/", + "cd %(builddir)s/lbm && chmod -R u+w . && ./01_BasicLBM 01_BasicLBM.prm", +] + +moduleclass = 'chem' From 2dd24eef47a24dc5f6f17a04ce386fa054c7b5ad Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 9 Oct 2024 13:25:14 +0200 Subject: [PATCH 098/524] adding easyconfigs: Stellarscope-1.4.1-foss-2023a.eb --- .../Stellarscope-1.4.1-foss-2023a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb b/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb new file mode 100644 index 00000000000..27dd6fd92b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Stellarscope' +version = '1.4.1' + +homepage = 'https://github.com/nixonlab/stellarscope' +description = """Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('Pysam', '0.22.0'), + ('HTSlib', '1.18'), + ('intervaltree-python', '3.1.0'), + ('SAMtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/nixonlab/stellarscope/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['64aa3fa30e9ee1d4857572a0f491fd4983c15a5b5906edf9a3b7cacda780b99c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/stellarscope'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["stellarscope -h"] + +moduleclass = 'bio' From 43321a606ff07af181432e122a59fe53599ab71b Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 9 Oct 2024 13:38:35 +0200 Subject: [PATCH 099/524] Added bokeh to the gfbf-2024a toolchain and tornado (dep of bokeh) to the GCCcore-13.3.0 toolchain --- .../b/bokeh/bokeh-3.6.0-gfbf-2024a.eb | 46 +++++++++++++++++++ .../t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb | 29 ++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb new file mode 100644 index 00000000000..fbdb34a71b6 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.6.0' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('matplotlib', '3.9.2'), + ('PyYAML', '6.0.2'), + ('Pillow-SIMD', '10.4.0'), + ('tornado', '6.4.1'), +] + +use_pip = True + +exts_list = [ + ('xyzservices', '2024.4.0', { + 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d4266c8c1c9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.4.1" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "13.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-6.1_increase-default-timeouts.patch'] +checksums = [ + {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, +] + +builddependencies = [ + ("binutils", "2.42"), +] +dependencies = [ + ("Python", "3.12.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" From 5762e6283e980919a62bcecf36ff200472169f51 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 9 Oct 2024 17:06:30 +0200 Subject: [PATCH 100/524] adding easyconfigs: Solids4foam-2.1-foss-2023a.eb --- .../Solids4foam/Solids4foam-2.1-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb new file mode 100644 index 00000000000..b74beba6c68 --- /dev/null +++ b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'Binary' + +name = 'Solids4foam' +version = '2.1' + +homepage = 'https://www.solids4foam.com/' +description = 'A toolbox for performing solid mechanics and fluid-solid interactions in OpenFOAM.' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/solids4foam/solids4foam/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['354dad483f8b086d64bf294829cf6fdf1e5784fd615578acff753791f2f391ca'] + +dependencies = [ + ('OpenFOAM', 'v2312'), + ('gnuplot', '5.4.8'), +] + +extract_sources = True + +install_cmd = 'source $FOAM_BASH && ' +# variables of target install directory +install_cmd += 'export WM_PROJECT_USER_DIR=%(installdir)s && ' +install_cmd += 'export FOAM_USER_APPBIN=%(installdir)s/bin && ' +install_cmd += 'export FOAM_USER_LIBBIN=%(installdir)s/lib && ' +install_cmd += 'export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && ' +install_cmd += 'export S4F_NO_FILE_FIXES=1 && ./Allwmake -j %(parallel)s' +# copy tests +install_cmd += ' && cp -av tutorials %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/solids4Foam'], + 'dirs': ['lib'], +} +sanity_check_commands = [ + 'source $FOAM_BASH && cd %(installdir)s/tutorials && ./Alltest' +] + +modloadmsg = "Please run 'source $FOAM_BASH' before using Solids4foam." + +moduleclass = 'chem' From f53954b22d6477e9c725e319e25e89592b7bca3d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:23:52 +0200 Subject: [PATCH 101/524] Add gnuplot --- .../g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 47 +++++++++++++++++++ .../l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb | 28 +++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb | 36 ++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..049c6e4a741 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '6.0.1' + +homepage = 'http://gnuplot.sourceforge.net' +description = "Portable interactive, function plotting utility" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [('https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] +dependencies = [ + ('ncurses', '6.5'), + ('cairo', '1.18.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('libgd', '2.3.3'), + ('Pango', '1.54.0'), + ('libcerf', '2.4'), + ('X11', '20240607'), + ('Qt6', '6.7.2'), + ('Lua', '5.4.7'), +] + +preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' +preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' +#configopts = "--with-qt=qt5 --without-latex --disable-wxwidgets" +configopts = "--without-latex --disable-wxwidgets" + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +# make sure that pdf terminal type is available +sanity_check_commands = ["%(name)s -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..98e622129cd --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.7' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9fbf5e28ef86c69858f6d3d34eccc32e911c1a28b4120ff3e84aaa70cfbf1e30'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), + ('libreadline', '8.2'), +] + + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..28e596386fd --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('fontconfig', '2.15.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' From 60a35617dd841278c8b749711246b954150a6a7c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:45:11 +0200 Subject: [PATCH 102/524] Fix style --- .../easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 301f804cc82..2674dfe8508 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -30,7 +30,19 @@ dependencies = [ ('gperftools', '2.16'), ] -configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " +configopts = '-DCMAKE_CXX_COMPILER=g++ ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DHPX_WITH_MALLOC=tcmalloc ' +configopts += '-DHPX_WITH_HWLOC=TRUE ' +configopts += '-DHPX_WITH_GOOGLE_PERFTOOLS=TRUE ' +configopts += '-DHPX_WITH_NETWORKING=TRUE ' +configopts += '-DHPX_WITH_PARCELPORT_TCP=FALSE ' +configopts += '-DHPX_WITH_PARCELPORT_MPI=TRUE ' +configopts += '-DHPX_WITH_TESTS=FALSE ' +configopts += '-DHPX_WITH_EXAMPLES=TRUE ' +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=128' #this should be handled by a hook for the system +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=' + os.cpu_count() +configopts += '-DHPX_WITH_FETCH_ASIO=TRUE ' bin_lib_subdirs = ['lib/%(namelower)s/'] From 00c9a50b45d1cd570060051e9f273ac6f12633b3 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:49:06 +0200 Subject: [PATCH 103/524] Add checksum --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 2674dfe8508..9e1c986fa71 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -17,6 +17,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/STEllAR-GROUP/%(namelower)s/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['5720ed7d2460fa0b57bd8cb74fa4f70593fe8675463897678160340526ec3c19'] builddependencies = [ ('CMake', '3.29.3'), @@ -30,6 +31,8 @@ dependencies = [ ('gperftools', '2.16'), ] +build_type = 'Release' + configopts = '-DCMAKE_CXX_COMPILER=g++ ' configopts += '-DCMAKE_BUILD_TYPE=Release ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' From e5644822f6c8086473968a499955bf0530d1516e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:55:29 +0200 Subject: [PATCH 104/524] Fix style --- easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb index 28e596386fd..2c03aa92105 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb @@ -23,8 +23,8 @@ dependencies = [ ('zlib', '1.3.1'), ] -configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" - +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" sanity_check_paths = { 'files': ['lib/%(name)s.a', 'lib/%(name)s.so'], From df0790f5535260a6edd4438ac6284494ba8bd442 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 9 Oct 2024 23:11:09 +0200 Subject: [PATCH 105/524] Update gnuplot-6.0.1-GCCcore-13.3.0.eb --- easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index 049c6e4a741..684924b80d1 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -32,7 +32,6 @@ dependencies = [ preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' -#configopts = "--with-qt=qt5 --without-latex --disable-wxwidgets" configopts = "--without-latex --disable-wxwidgets" From 8c81ac8aeea09758d87e088ec53fdabc6338e4bc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 10 Oct 2024 09:32:57 +0200 Subject: [PATCH 106/524] update checksum --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index a11cf7fed7c..e67d5c98ae7 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -18,7 +18,7 @@ sources = [{ 'recursive': True, } }] -checksums = ['0c6fbcc4897573ec24ee4e0c60a0a6fa3e20f7f4db513e89689a1638a0a6cd1d'] +checksums = ['8b9526fad303346ebcf389308b2618dfeb592826b425f725414859dfd8625240'] dependencies = [ ('PASA', '2.5.3',), From dfc4bf00502f883a12fd946af35530d0ea694b40 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 10 Oct 2024 10:01:00 +0200 Subject: [PATCH 107/524] set checksum to None as done fort other source that use "recursive": True --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index e67d5c98ae7..ee86c8a1dd6 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -18,7 +18,7 @@ sources = [{ 'recursive': True, } }] -checksums = ['8b9526fad303346ebcf389308b2618dfeb592826b425f725414859dfd8625240'] +checksums = [None] dependencies = [ ('PASA', '2.5.3',), From ca2fc7f4a43480ca9e5cbc4eb83f0c661182c808 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 10:09:33 +0200 Subject: [PATCH 108/524] Fix style --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index 684924b80d1..c0f7a2a4d89 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -30,8 +30,12 @@ dependencies = [ ('Lua', '5.4.7'), ] -preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' +preconfigopts = 'autoreconf && ' + +# make sure that right Lua library is used (bypassing pkg-config) +preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' + configopts = "--without-latex --disable-wxwidgets" From c454e67956564a6f760c7a5407434ec921cd3a6f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 10:22:00 +0200 Subject: [PATCH 109/524] Add comment --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index c0f7a2a4d89..e27fc37776f 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -34,11 +34,12 @@ preconfigopts = 'autoreconf && ' # make sure that right Lua library is used (bypassing pkg-config) preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' + +# fix undefined reference to symbol 'libiconv_open' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' configopts = "--without-latex --disable-wxwidgets" - sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [], From 43423f061785d27caafe64290ce58bea2de3ebe1 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 10 Oct 2024 11:03:36 +0200 Subject: [PATCH 110/524] add Eigen as builddep --- .../easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb index b74beba6c68..a633cd6d2f0 100644 --- a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb @@ -12,6 +12,7 @@ source_urls = ['https://github.com/solids4foam/solids4foam/archive/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['354dad483f8b086d64bf294829cf6fdf1e5784fd615578acff753791f2f391ca'] +builddependencies = [('Eigen', '3.4.0')] dependencies = [ ('OpenFOAM', 'v2312'), ('gnuplot', '5.4.8'), @@ -25,6 +26,7 @@ install_cmd += 'export WM_PROJECT_USER_DIR=%(installdir)s && ' install_cmd += 'export FOAM_USER_APPBIN=%(installdir)s/bin && ' install_cmd += 'export FOAM_USER_LIBBIN=%(installdir)s/lib && ' install_cmd += 'export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && ' +install_cmd += 'export EIGEN_DIR=$EBROOTEIGEN && ' install_cmd += 'export S4F_NO_FILE_FIXES=1 && ./Allwmake -j %(parallel)s' # copy tests install_cmd += ' && cp -av tutorials %(installdir)s' From 71273e489e5d13584714557a6ac328b308ada47a Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 10 Oct 2024 11:19:11 +0200 Subject: [PATCH 111/524] Added cuDNN and cuTENSOR --- .../c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb | 32 +++++++++++++++ .../c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb | 40 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a6cbe9ef7e7 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb @@ -0,0 +1,32 @@ +name = 'cuDNN' +version = '9.5.0.50' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d'] + +dependencies = [('CUDA', '12.6.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_static.a', 'lib64/libcudnn_cnn_static.a', + 'lib64/libcudnn_engines_precompiled_static.a', 'lib64/libcudnn_engines_runtime_compiled_static.a', + 'lib64/libcudnn_graph_static.a', 'lib64/libcudnn_heuristic_static.a', 'lib64/libcudnn_ops_static.a', + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb new file mode 100644 index 00000000000..fe7b69ac9b0 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +version = '2.0.2.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-%(arch)s/' +] +sources = ['libcutensor-linux-%(arch)s-%(version)s-archive.tar.xz'] + +checksums = [{ + 'libcutensor-linux-sbsa-%(version)s-archive.tar.xz': + '5163dd40f11f328e469a6d9b0056c8346f5d59ed538c18d6b954e4ae657c69cc', + 'libcutensor-linux-x86_64-%(version)s-archive.tar.xz': + '0e957ae7b352f599de34b6fa1ba999b0617887f885d7436ac5737d71a6b83baa', +}] + +local_cudamajver = '12' +dependencies = [('CUDA', '12.6.0')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From 8314b835231f14a146e2b5d199d4b66199e0389e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 10 Oct 2024 12:28:29 +0200 Subject: [PATCH 112/524] Fixed typo in filename of cuTENSOR --- ...uTENSOR-2.0.2.5-CUDA-12.eb => cuTENSOR-2.0.2.5-CUDA-12.6.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cuTENSOR/{cuTENSOR-2.0.2.5-CUDA-12.eb => cuTENSOR-2.0.2.5-CUDA-12.6.0.eb} (100%) diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb similarity index 100% rename from easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb rename to easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb From 262ac6f4dd6be6aed723343957a8ecef13c48cd0 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 15:27:14 +0200 Subject: [PATCH 113/524] Add QuantumESPRESSO and libxc --- .../l/libxc/libxc-6.2.2-GCC-13.3.0.eb | 52 ++++++ .../QuantumESPRESSO-7.3.1-foss-2024a.eb | 159 ++++++++++++++++++ 2 files changed, 211 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..9e4de5e8082 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://gitlab.com/%(name)s/%(name)s/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [ + ('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc', + 'd1b65ef74615a1e539d87a0e6662f04baf3a2316706b4e2e686da3193b26b20f'), +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb new file mode 100644 index 00000000000..8cbd539a51d --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb @@ -0,0 +1,159 @@ +name = 'QuantumESPRESSO' +version = '7.3.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +# Different from the one at tag qe-7.3.1 because of: +# https://github.com/dceresoli/qe-gipaw/issues/19 +local_qe_gipaw_hash = "79d3a03b7bdc4325e66f3fad02a24c6e6e3e5806" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('ELPA', '2024.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [ + "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] From 677666a2b785d8961cfa75f2a1292753e2c48d23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 10 Oct 2024 15:49:13 +0200 Subject: [PATCH 114/524] adding easyconfigs: PySCF-2.7.0-foss-2023a.eb, NECI-20230620-foss-2023a.eb, tblis-20230422-foss-2023a.eb --- .../n/NECI/NECI-20230620-foss-2023a.eb | 51 +++++++ .../p/PySCF/PySCF-2.7.0-foss-2023a.eb | 138 ++++++++++++++++++ .../t/tblis/tblis-20230422-foss-2023a.eb | 26 ++++ 3 files changed, 215 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb new file mode 100644 index 00000000000..cc48f534ee8 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20230620' +_commit = '558e88c5ae6c30d0505a9badbc69111be0866ba1' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +dependencies = [ + ('HDF5', '1.14.0'), +] + +# disable tests ending up with SEGFAULT +preconfigopts = "sed -i '/back_spawn_excit_gen/d' '%(builddir)s/NECI_STABLE/unit_tests/CMakeLists.txt' && " + +# enable support for HDF5 +configopts = "-DENABLE_HDF5=ON" + +test_cmd = 'ctest' +runtest = '-j' + +files_to_copy = ['bin', 'lib', (['modules'], 'include')] + +_binaries = ['dneci', 'kdneci', 'kmneci', 'kneci', 'mneci', 'neci'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/lib%s.a' % x for x in _binaries], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb new file mode 100644 index 00000000000..72432ce1b97 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb @@ -0,0 +1,138 @@ +easyblock = 'CMakeMakeCp' +name = 'PySCF' +version = '2.7.0' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2f94e6dae8556085bb765eb5250f61589e977b4f12540c748241101d40da241'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), # needed by zquatev +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy, scipy + ('h5py', '3.9.0'), + ('libcint', '5.4.0'), + ('libxc', '6.2.2'), + ('XCFun', '2.1.1'), + ('CPPE', '0.3.3a0'), # extra + ('PyBerny', '0.6.3'), # extra + ('PyCheMPS2', '1.8.12'), # needed by dmrgscf + ('Block', '1.5.3-20200525'), # needed by dmrgscf + ('NECI', '20230620'), # needed by fciqmc + ('Dice', '20240702'), # needed by icmpspt + ('tblis', '20230422'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'modulename': 'pyscf.%(name)s', + 'source_urls': ['https://github.com/pyscf/%(name)s/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], +} + +# The following list of extensions is equivalent to installing PySCF with extras: +# all + dmrgscf + fciqmcscf + hci + mbd + tblis + zquatev +exts_list = [ + ('dftd3', '94091d8', { + 'checksums': ['a69ae44b3d02d2c06fd531373f20ee1251ef27fc932d40a7cafea6c09d8784fc'], + }), + ('doci', '08079a9', { + 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], + }), + ('icmpspt', '50c386e', { + 'patches': [('PySCF-2.1.1_icmpspt-exe-path.patch', 0)], + 'checksums': [ + {'icmpspt-50c386e.tar.gz': '08029863ae8740939a730fe5e104661c67d8dd0b8a8555b603fc8a0777096d48'}, + {'PySCF-2.1.1_icmpspt-exe-path.patch': 'e972e377b34b964c48a99909301bf21a9c73d8eb9ecb96a889621d71471c56c9'}, + ], + }), + ('properties', '8b94d8d', { + 'modulename': 'pyscf.prop', + 'checksums': ['b40e071472a6bdfcaec8cd358c7c58c58748c59d8b188fdca09d6eca63329914'], + }), + ('qsdopt', '3ad2c02', { + 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], + }), + ('semiempirical', '470d716', { + 'checksums': ['0bbe304867fd053ed647445ac84c4c76787ad23def9f72415aec297740121eef'], + }), + ('shciscf', '7edb54d', { + 'checksums': ['ae54265f6600b73a350b00274c95bb0de940ddcd6e1b47b434594e18136b1bed'], + }), + ('MCfun', '0.2.3', { + 'modulename': 'mcfun', + 'source_urls': ['https://github.com/Multi-collinear/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3741b49b839df0fde891d51292520ed9094fa1d3c9b5d9c042d4f26087cf6a13'], + }), + ('pyqmc', '0.6.0', { + 'modulename': 'pyqmc', + 'source_urls': ['https://github.com/WagnerGroup/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6e9f612c2d0bf2198154520e01dce57cf3a6e474840c1892466de3171eaeb7db'], + }), + ('dmrgscf', 'a03f7b6', { + 'patches': [('PySCF-2.1.1_dmrgscf-settings.patch', 0)], + 'checksums': [ + {'dmrgscf-a03f7b6.tar.gz': 'dee40abe3d2aebab7a2d0eade4e464a6ae851b4c2b49a2cde4c3aa88f0651b04'}, + {'PySCF-2.1.1_dmrgscf-settings.patch': 'a0310a2a90e96bd64d1560b2cc73a805717e129d2921e91cc5e6038b9f153677'}, + ], + }), + ('fciqmc', 'ee98fb4', { + 'modulename': 'pyscf.fciqmcscf', + 'checksums': ['b2f081ac295df0e622c6d1b3bff6d7834f97131f1f0fc87ec8bcff2137ef4199'], + }), + ('mbd', '485c18c', { + 'patches': [('PySCF-2.1.1_mbd-fix-init.patch', 0)], + 'checksums': [ + {'mbd-485c18c.tar.gz': 'de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'}, + {'PySCF-2.1.1_mbd-fix-init.patch': '4f8e4b2e39b77428187851c4b6ced39401561bc81f4f3a4605da5d5c7b798cbc'}, + ], + }), + ('naive-hci', '0c28d6e', { + 'modulename': 'pyscf.hci', + 'checksums': ['de247d17b80133655df5966341e5adb691b0df150cd9b0f1980cf62ec55229d5'], + }), + ('tblis', 'c67c8af', { + 'modulename': 'pyscf.tblis_einsum', + # Use our `tblis`. + 'preinstallopts': 'CMAKE_CONFIGURE_ARGS="-DVENDOR_TBLIS=off" ', + 'source_urls': ['https://github.com/pyscf/pyscf-tblis/archive/'], + 'checksums': ['9a40a760e3be1d0b7f49faab5897388dcdf75094f75e06b4c344b3642a0401d6'], + }), + ('zquatev', '4eb41b1', { + 'modulename': 'zquatev', + 'preinstallopts': "sed -i 's/add_subdirectory(pybind11)/find_package(pybind11 REQUIRED)/' CMakeLists.txt && ", + 'source_urls': ['https://github.com/sunqm/%(name)s/archive/'], + 'checksums': ['4caf08e3831a5d86e6bc22f3b4028cc159101cb9658d09de16e382e268a5a2e9'], + }), +] + +start_dir = 'pyscf/lib' +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +_py_site_packages = 'lib/python%(pyshortver)s/site-packages' +files_to_copy = [(['pyscf'], _py_site_packages)] + +sanity_check_paths = { + 'files': [_py_site_packages + '/pyscf/__init__.py'], + 'dirs': [_py_site_packages + d for d in ['/pyscf/data', '/pyscf/lib']], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': _py_site_packages} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb new file mode 100644 index 00000000000..a9853cde523 --- /dev/null +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tblis' +version = '20230422' +local_commit = '4de1919' + +homepage = "https://github.com/devinamatthews/tblis" +description = """TBLIS is a library and framework for performing tensor + operations, especially tensor contraction, using native algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/devinamatthews/tblis/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['85b72884022edd2612e3a0b3ed12aa6237d3989b581091d21f58124a7450aaeb'] + +sanity_check_paths = { + 'files': [ + 'include/tblis/tblis.h', + 'lib/libtblis.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'lib' From c1cd88734b4d4b73b76cd917d1844f45ab333dfe Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 10 Oct 2024 17:35:10 +0200 Subject: [PATCH 115/524] add M4 dep --- .../easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb index a633cd6d2f0..900ee008508 100644 --- a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [('Eigen', '3.4.0')] dependencies = [ ('OpenFOAM', 'v2312'), ('gnuplot', '5.4.8'), + ('M4', '1.4.19'), ] extract_sources = True From d4c73daa3d41a29caed50a5568a788c2296a6143 Mon Sep 17 00:00:00 2001 From: crivella Date: Thu, 10 Oct 2024 17:49:02 +0200 Subject: [PATCH 116/524] Added EC for libffi-3.4.5 SYSTEM --- .../easyconfigs/l/libffi/libffi-3.4.5.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb new file mode 100644 index 00000000000..df82da05952 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.5' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fff4e589e3b239d888d9aa44b3ff30693c2ba1617f953925a70ddebcc102b2'] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 256cbef1db43fe7491b09204d300a7b41ce43f00 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 10 Oct 2024 17:55:46 +0200 Subject: [PATCH 117/524] adding easyconfigs: EvidentialGene-2018.01.01-gompi-2023a.eb --- .../EvidentialGene-2018.01.01-gompi-2023a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb new file mode 100644 index 00000000000..15d8b4dc07c --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2018.01.01' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['6972108112cdb1fb106da11321d06b09f518b544e4739d0bf19da1984131e221'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' From 3c9d1f112f705228f5d36b6d3139f155437e4601 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Oct 2024 18:13:08 +0200 Subject: [PATCH 118/524] remove Ringo v1.66.0 from R-bundle-Bioconductor v3.19 Co-authored-by: Alexander Grund --- .../R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb index 6e3261a44b0..f426b6ffbc5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb @@ -729,9 +729,6 @@ exts_list = [ ('gsmoothr', '0.1.7', { 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], }), - ('Ringo', '1.66.0', { - 'checksums': ['adc7f824026aff62b36a71827ef815e11d4cb92a94762e0320248649da5400b2'], - }), ('R.devices', '2.17.2', { 'checksums': ['403eeaf552dd696142096973dee3460dc52c19b73fd194841dd4638e2bdcec95'], }), From db3f966d9fd2115758fe4031ac4188bf8b5a3ddf Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 11 Oct 2024 10:06:35 +0200 Subject: [PATCH 119/524] Removed sympy since it is already merged for this toolchain with a newer version. --- .../s/sympy/sympy-1.13.2-gfbf-2024a.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb deleted file mode 100644 index 58034bd1d90..00000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.13.2-gfbf-2024a.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'sympy' -version = '1.13.2' - -homepage = 'https://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'gfbf', 'version': '2024a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['401449d84d07be9d0c7a46a64bd54fe097667d5e7181bfe67ec777be9e01cb13'] - -dependencies = [ - ('Python', '3.12.3'), - ('SciPy-bundle', '2024.05'), - ('gmpy2', '2.2.0'), -] - - -moduleclass = 'math' From b2651fc36941cddd10b38a0a446b371a83d5d258 Mon Sep 17 00:00:00 2001 From: thoffman Date: Fri, 11 Oct 2024 10:44:34 +0200 Subject: [PATCH 120/524] update dm-haiku to 0.0.12; @akesandgren suggestions --- .../AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb | 14 ++--- .../AlphaFold-2.3.2_BioPythonPDBData.patch | 14 +++++ .../dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb | 62 +++++++++++++++++++ 3 files changed, 83 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb index 44e43d11b86..64b71b8f123 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), - ('TensorFlow', '2.13.0'), # doesn't require TF-gpu + ('TensorFlow', '2.15.1'), # doesn't require TF-gpu ('Biopython', '1.83'), ('HH-suite', '3.3.0'), ('HMMER', '3.4'), @@ -29,7 +29,7 @@ dependencies = [ ('NCCL', '2.18.3', versionsuffix), ('OpenMM', '8.0.0', versionsuffix), ('dm-tree', '0.1.8'), - ('dm-haiku', '0.0.11', versionsuffix), + ('dm-haiku', '0.0.12', versionsuffix), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, @@ -84,16 +84,16 @@ exts_list = [ 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], }), (name, version, { + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'patches': [ 'AlphaFold-2.0.0_fix-packages.patch', 'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch', 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', 'AlphaFold-2.3.2_use_openmm_8.0.0.patch', - 'AlphaFold-2.3.2_BioPythonSCOPData.patch', + 'AlphaFold-2.3.2_BioPythonPDBData.patch', ], - 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ {'AlphaFold-2.3.2.tar.gz': '4ea8005ba1b573fa1585e4c29b7d188c5cbfa59b4e4761c9f0c15c9db9584a8e'}, {'AlphaFold-2.0.0_fix-packages.patch': '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db'}, @@ -104,8 +104,8 @@ exts_list = [ '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'}, {'AlphaFold-2.3.2_use_openmm_8.0.0.patch': 'bbef940c0c959040aaf3984ec47777a229c164517b54616a2688d58fae636d84'}, - {'AlphaFold-2.3.2_BioPythonSCOPData.patch': - '5aedd5a35da6d0a993ca19f4de807cf77ec36a5a52c97100110a0c5475cef1b8'}, + {'AlphaFold-2.3.2_BioPythonPDBData.patch': + 'e4483a525ae5c4dc5a5f633bed8cf5337c329e64b603ab7b684a9d18cd26a22f'}, ], }), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch new file mode 100644 index 00000000000..df73873cb1c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch @@ -0,0 +1,14 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/10 +# BioPython 1.83 does not provide protein_letters_3to1 in Bio.Data.SCOPdata but in Bio.Data.PDBData (and Bio.Data.IUPACData) +diff -ru -ru alphafold-2.3.2/alphafold/data/mmcif_parsing.py alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py +--- alphafold-2.3.2/alphafold/data/mmcif_parsing.py 2024-02-19 09:55:16.359778490 +0100 ++++ alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py 2023-03-27 13:50:49.000000000 +0200 +@@ -21,7 +21,7 @@ + + from absl import logging + from Bio import PDB +-from Bio.Data import SCOPData ++from Bio.Data import PDBData as SCOPData + + # Type aliases: + ChainId = str diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3adbc9b5119 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,62 @@ +# update 0.9.11: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.12' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py + ('PyYAML', '6.0'), + ('CUDA', '12.1.1', '', SYSTEM), + ('tensorstore', '0.1.53'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True +# flax > 0.8.5 req jax >= 0.4.27 +# optax 0.2.3 req. jax >= 0.4.27 +# orbax_checkpoint 0.5.18 req. jax >=0.4.25 +# orbax_checkpoint 0.5.19 req. jax >=0.4.26 + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), + ('optax', '0.2.2', { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.18', { + 'modulename': 'orbax.checkpoint', + 'preinstallopts': """sed -i 's/jax >= 0.4.25/&\\*/g' pyproject.toml &&""", + 'checksums': ['29f5d311b412760bd6a2fecab3bdbf75407bc00dc6d0457d19478258ecc8fa6d'], + }), + ('toolz', '1.0.0', { + 'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['ba0b3acf71433156737fe342c486da11727e5e6c9e054245f4f9b8f0b53eb608'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 572eb15bbf596e42002e76548ffb9b0db4cd977a Mon Sep 17 00:00:00 2001 From: thoffman Date: Fri, 11 Oct 2024 10:51:39 +0200 Subject: [PATCH 121/524] sanity_check_commands order --- .../a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb index 64b71b8f123..470e97fec2d 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -130,8 +130,8 @@ sanity_check_commands = [ "pdbfixer --help", "python -m openmm.testInstallation", "python -c 'import alphafold'", - "python %(installdir)s/bin/run_alphafold_test.py", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", + "python %(installdir)s/bin/run_alphafold_test.py", ] sanity_pip_check = True From 030559ad5780ede4b51e86476c0b452ddc2ad788 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:02:43 +0200 Subject: [PATCH 122/524] Update dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb --- .../d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb index 3adbc9b5119..781cb015145 100644 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb @@ -1,4 +1,4 @@ -# update 0.9.11: Thomas Hoffmann (EMBL) +# update 0.0.12: Thomas Hoffmann (EMBL) easyblock = 'PythonBundle' name = 'dm-haiku' From 04513f50ad2122babfddbec8f92d594cc7cb24a7 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:03:28 +0200 Subject: [PATCH 123/524] Delete easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb --- .../dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index a30f458a967..00000000000 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,57 +0,0 @@ -# update 0.9.11: Thomas Hoffmann (EMBL) -easyblock = 'PythonBundle' - -name = 'dm-haiku' -version = '0.0.11' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://github.com/deepmind/dm-haiku' -description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural -network library for TensorFlow.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py - ('PyYAML', '6.0'), - ('CUDA', '12.1.1', '', SYSTEM), - ('tensorstore', '0.1.53'), - ('protobuf-python', '4.24.0'), -] - -use_pip = True - -exts_list = [ - ('jmp', '0.0.4', { - 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], - }), - ('flax', '0.8.1', { - 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], - }), - ('optax', '0.1.9', { - 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], - }), - ('orbax_checkpoint', '0.5.3', { - 'modulename': 'orbax', - 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], - }), - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('chex', '0.1.85', { - 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], - }), - ('nest_asyncio', '1.6.0', { - 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], - }), - (name, version, { - 'modulename': 'haiku', - 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From 34926ebf1f9fa3c28950be1f5b060c48b05a60c8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:04:41 +0200 Subject: [PATCH 124/524] Delete easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch --- .../AlphaFold-2.3.2_BioPythonSCOPData.patch | 14 -------------- 1 file changed, 14 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch deleted file mode 100644 index 893b7f0483f..00000000000 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonSCOPData.patch +++ /dev/null @@ -1,14 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 -# BioPython 1.83 does not provide protein_letters_3to1 in Bio.Data.SCOPdata but in Bio.Data.IUPACData -diff -ru -ru alphafold-2.3.2/alphafold/data/mmcif_parsing.py alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py ---- alphafold-2.3.2/alphafold/data/mmcif_parsing.py 2024-02-19 09:55:16.359778490 +0100 -+++ alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py 2023-03-27 13:50:49.000000000 +0200 -@@ -21,7 +21,7 @@ - - from absl import logging - from Bio import PDB --from Bio.Data import SCOPData -+from Bio.Data import IUPACData as SCOPData - - # Type aliases: - ChainId = str From 4fee5a77b0db24ee5c0b5de10338fdc478f2dcb8 Mon Sep 17 00:00:00 2001 From: thoffman Date: Fri, 11 Oct 2024 12:34:32 +0200 Subject: [PATCH 125/524] revert TF to ver 2.13.0; uniref30 default version env var --- .../AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb | 26 +-- ....3.2_data-dep-paths-shebang-UniRef30.patch | 164 ++++++++++++++++++ 2 files changed, 179 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb index 470e97fec2d..85fd26e21f7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), - ('TensorFlow', '2.15.1'), # doesn't require TF-gpu + ('TensorFlow', '2.13.0'), # doesn't require TF-gpu ('Biopython', '1.83'), ('HH-suite', '3.3.0'), ('HMMER', '3.4'), @@ -84,21 +84,21 @@ exts_list = [ 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], }), (name, version, { - 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'patches': [ 'AlphaFold-2.0.0_fix-packages.patch', - 'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch', + 'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch', 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', 'AlphaFold-2.3.2_use_openmm_8.0.0.patch', 'AlphaFold-2.3.2_BioPythonPDBData.patch', ], + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ {'AlphaFold-2.3.2.tar.gz': '4ea8005ba1b573fa1585e4c29b7d188c5cbfa59b4e4761c9f0c15c9db9584a8e'}, {'AlphaFold-2.0.0_fix-packages.patch': '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db'}, - {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch': - '72a7b7cb8be4105f7bd32b404454afa465300d16b1ccc9933c9a70873f134f4e'}, + {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch': + '58cd0ce4094afe76909649abe68034c4fbdb500967f5c818f49b530356dc012b'}, {'AlphaFold-2.0.0_n-cpu.patch': 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04'}, {'AlphaFold-2.0.1_setup_rm_tfcpu.patch': '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'}, @@ -151,13 +151,17 @@ modextravars = { # # Download with $EBROOTALPHAFOLD/scripts/download_all_data.sh /path/to/AlphaFold_DBs/$EBVERSIONALPHAFOLD 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs/%(versions)s', # please adapt + # Adapt in order to use a different version of UniRef30 by default, + # e.g., v2023_02 from https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz: + 'ALPHAFOLD_UNIREF30_VER': '2021_03', 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 } -modloadmsg = """Unlike previous modules, this module is using the updated UniRef30_2023_02 by default! -In order to use the old UniRef30, please explicitly pass the command line parameter: ---uniref30_database_path $ALPHAFOLD_DATA_DIR/uniref30/UniRef30_2021_03""" - -# Remark: Please modify $EBROOTALPHAFOLD/scripts/download_uniref30.sh in order to download old UniRef30 2021.03 +postinstallmsgs = [ + "A newer version of UniRef30 (2023_02) is available at: " + "https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz. " + "Untar to $ALPHAFOLD_DATA_DIR/uniref30/ and set the default version accordingly by changing " + "modextravars:ALPHAFOLD_UNIREF30_VER." +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch new file mode 100644 index 00000000000..c7bbd59ac0c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch @@ -0,0 +1,164 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0/2.1.2/2.3.0/2.3.2: Thomas Hoffmann (EMBL); +uniref30 version env. variable (THEMBL) + +diff -ru alphafold-2.3.2/run_alphafold.py alphafold-2.3.2_data-dep-paths-shebang-UniRef30/run_alphafold.py +--- alphafold-2.3.2/run_alphafold.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_data-dep-paths-shebang-UniRef30/run_alphafold.py 2024-10-11 11:34:06.330278962 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + # Copyright 2021 DeepMind Technologies Limited + # + # Licensed under the Apache License, Version 2.0 (the "License"); +@@ -42,6 +43,48 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++uniref30_ver = os.getenv('ALPHAFOLD_UNIREF30_VER') ++if not uniref30_ver: uniref30_ver = '2021_03' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_%s' % uniref30_ver) ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -59,7 +102,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -71,32 +114,32 @@ + flags.DEFINE_string('hmmsearch_binary_path', shutil.which('hmmsearch'), + 'Path to the hmmsearch executable.') + flags.DEFINE_string('hmmbuild_binary_path', shutil.which('hmmbuild'), +- 'Path to the hmmbuild executable.') ++ 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), +- 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' +- 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' +- 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' +- 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' +- 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' +- 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' +- 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' +- 'template mmCIF structures, each named .cif') ++ 'Path to the Kalign executable.') ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' ++ 'version of BFD used with the "reduced_dbs" preset.') ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' ++ 'database for use by JackHMMer.') ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' ++ 'database for use by HHsearch.') ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' ++ 'seqres database for use by hmmsearch.') ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' ++ 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' +- 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' +- 'mapping from obsolete PDB IDs to the PDB IDs of their ' +- 'replacements.') ++ 'to consider. Important if folding historical test sets.') ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' ++ 'mapping from obsolete PDB IDs to the PDB IDs of their ' ++ 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', + ['full_dbs', 'reduced_dbs'], + 'Choose preset MSA database configuration - ' +@@ -137,7 +180,7 @@ + 'distracting stereochemical violations but might help ' + 'in case you are having issues with the relaxation ' + 'stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -334,6 +377,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -456,13 +503,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) From 5c938cfad23f545a726f05e2e276fd699c981267 Mon Sep 17 00:00:00 2001 From: thoffman Date: Fri, 11 Oct 2024 12:36:19 +0200 Subject: [PATCH 126/524] update tensorstore to 0.1.65 --- .../dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb | 2 +- .../tensorstore-0.1.65-foss-2023a.eb | 62 +++++++++++++++++++ 2 files changed, 63 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb index 781cb015145..e5ef56de773 100644 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py ('PyYAML', '6.0'), ('CUDA', '12.1.1', '', SYSTEM), - ('tensorstore', '0.1.53'), + ('tensorstore', '0.1.65'), ('protobuf-python', '4.24.0'), ] diff --git a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb new file mode 100644 index 00000000000..5dd271c0d88 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb @@ -0,0 +1,62 @@ +# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/10 +easyblock = 'PythonBundle' + +name = 'tensorstore' +version = '0.1.65' + +homepage = 'https://github.com/google/tensorstore' +description = """TensorStore is an open-source C++ and Python software library designed for +storage and manipulation of large multi-dimensional arrays.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('NASM', '2.16.01'), + ('pybind11', '2.11.1'), + ('Bazel', '6.3.1'), + + + + ('PyYAML', '6.0'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('snappy', '1.1.10'), + ('Brotli', '1.0.9'), + ('protobuf', '24.0'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('libwebp', '1.3.1'), + ('nlohmann_json', '3.11.2'), + ('Blosc', '1.21.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ml_dtypes', '0.3.2'), +] + +use_pip = True + + +local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" +local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" +local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? +local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" +local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" +# inject CFLAGS: +local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" + + +local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp + +exts_list = [ + (name, version, { + 'installopts': '-v', + 'preinstallopts': local_ts_preinstall, + 'checksums': ['65cbe5a600c32569bb0b9f597ea318cc298a13b42d5fc98168c97bb11f320eae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 02b773e74c15cb6a008ef8c52508c9c4e54c5717 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 11 Oct 2024 15:32:24 +0200 Subject: [PATCH 127/524] downgrade to gfbf and fix dependencies --- ....19.0-foss-2023a.eb => Gradio-4.19.0-gfbf-2023a.eb} | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/g/Gradio/{Gradio-4.19.0-foss-2023a.eb => Gradio-4.19.0-gfbf-2023a.eb} (94%) diff --git a/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb similarity index 94% rename from easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb rename to easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb index 4c3556a27cd..3f949981b52 100644 --- a/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-foss-2023a.eb +++ b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb @@ -9,12 +9,14 @@ Gradio is an open-source Python package that allows you to quickly build a demo application for your machine learning model, API, or any arbitrary Python function. """ -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('binutils', '2.40'), ('Rust', '1.75.0'), ('maturin', '1.4.0', '-Rust-1.75.0'), + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), ] dependencies = [ @@ -25,18 +27,12 @@ dependencies = [ ('matplotlib', '3.7.2'), ('Pillow', '10.0.0'), ('tqdm', '4.66.1'), - ('hatchling', '1.18.0'), - ('poetry', '1.5.1'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('hatch-requirements-txt', '0.4.1', { - 'source_tmpl': 'hatch_requirements_txt-%(version)s.tar.gz', - 'checksums': ['2c686e5758fd05bb55fa7d0c198fdd481f8d3aaa3c693260f5c0d74ce3547d20'], - }), ('aiofiles', '23.2.1', { 'checksums': ['84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a'], }), From 9852fe7458a6ee97fa5580d15015b9af03fb8a01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 11 Oct 2024 16:16:27 +0200 Subject: [PATCH 128/524] adding easyconfigs: Cellformer-20240917-foss-2023a-R-4.3.2.eb --- .../Cellformer-20240917-foss-2023a-R-4.3.2.eb | 188 ++++++++++++++++++ 1 file changed, 188 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..4f21285268a --- /dev/null +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -0,0 +1,188 @@ +easyblock = 'Tarball' + +name = 'Cellformer' +version = '20240917' +versionsuffix = '-R-%(rver)s' +local_commit = '99a1165' + +homepage = 'https://github.com/elo-nsrb/Cellformer' +description = '''An implementation of Cellformer from our publication: Berson et al. + "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature"''' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/elo-nsrb/Cellformer/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['7cbddad75a4d47dfc0a39cd660ef20fe4e3cb755631b1b96136c1c3d5226c914'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), + ('scikit-learn', '1.3.1'), + ('PyTorch-Lightning', '2.2.1'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('SciPy-bundle', '2023.07'), + ('Seaborn', '0.13.2'), + ('tensorboard', '2.15.1'), + ('tensorboardX', '2.6.2.2'), + ('torchvision', '0.16.0'), + ('tqdm', '4.66.1'), + ('scanpy', '1.9.8'), + ('pretty-yaml', '24.7.0'), + ('Arrow', '14.0.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('ArchR', '1.0.2', versionsuffix), + ('typing-extensions', '4.9.0'), + ('einops', '0.7.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('typing_extensions', '4.12.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d'], + }), + ('asteroid_filterbanks', '0.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4932ac8b6acc6e08fb87cbe8ece84215b5a74eee284fe83acf3540a72a02eaf5'], + }), + ('huggingface_hub', '0.25.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1897caf88ce7f97fe0110603d8f66ac264e3ba6accdf30cd66cc0fed5282ad25'], + }), + ('julius', '0.2.7', { + 'checksums': ['3c0f5f5306d7d6016fcc95196b274cae6f07e2c9596eed314e4e7641554fbb08'], + }), + ('cached_property', '1.5.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0'], + }), + ('mir_eval', '0.7', { + 'checksums': ['e1febaa5766c65a7545c2a170b241490f47a98987370b1e06742424c5debe65e'], + }), + ('pesq', '0.0.4', { + 'checksums': ['b724b28f73fb638522982bd68e8c3c0957e2f45210639a460233b17aa7fc890b'], + }), + ('pb_bss_eval', '0.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a72c2fd04c9f4a4e734cf615029c3877e6e4536225eeaaae05bb0cf014b3af1b'], + }), + ('soundfile', '0.12.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['828a79c2e75abab5359f780c81dccd4953c45a2c4cd4f05ba3e233ddf984b882'], + }), + ('pytorch_ranger', '0.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1e69156c9cc8439185cb8ba4725b18c91947fbe72743e25aca937da8aeb0c8ec'], + }), + ('torch_optimizer', '0.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['b7adaed38b66a5c5105a59b30a71c4ab7c9954baf0acabd969fee3dac954657d'], + }), + ('pystoi', '0.4.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['e277b671663d26d35a2416c9c8010a74084e6c3970354506398051a554896939'], + }), + ('torch_stoi', '0.2.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6eee85e33b42fe843a2150de46000f72e7b87cbeb19ae6ab9bbd94b6ec6b3cd2'], + }), + ('torchmetrics', '1.4.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['76e67490231acef7f70cf36ab129df72fb2b0256dada7051001ab3b9f8699bf4'], + }), + ('asteroid', '0.7.0', { + 'checksums': ['0326f28c5342495cb08ba0520efd0e21e39435dfd78854837fdd5a6c9c9ca410'], + }), + ('everett', '3.1.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['db13891b849e45e54faea93ee79881d12458c5378f5b9b7f806eeff03ce1de3c'], + }), + ('configobj', '5.0.9', { + 'checksums': ['03c881bbf23aa07bccf1b837005975993c4ab4427ba57f959afdd9d1a2386848'], + }), + ('python_box', '6.1.0', { + 'modulename': 'box', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['bdec0a5f5a17b01fc538d292602a077aa8c641fb121e1900dff0591791af80e8'], + }), + ('sentry_sdk', '2.15.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8fb0d1a4e1a640172f31502e4503543765a1fe8a9209779134a4ac52d4677303'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('comet_ml', '3.47.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['81062bbef2d0758c8e77d8a469824d2c20ec13b09855c78b51b078203628b8c2'], + }), + ('fast_histogram', '0.14', { + 'checksums': ['390973b98af22bda85c29dcf6f008ba0d626321e9bd3f5a9d7a43e5690ea69ea'], + }), + ('mpl_scatter_density', '0.7', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['721b4efeafcbc0ba4a5c1ecd8f401dc2d1aa6a372445c5b49e1da34e70a95ead'], + }), + ('tensorboard_data_server', '0.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['753d4214799b31da7b6d93837959abebbc6afa86e69eacf1e9a317a48daa31eb'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('torchmetrics', '1.4.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87b9eca51ff6f93985a0f9db509f646cb45425b016f4d2f383d8c28d40dde5b6'], + }), + ('torchmetrics', '0.11.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['45f892f3534e91f3ad9e2488d1b05a93b7cb76b7d037969435a41a1f24750d9a'], + }), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +fix_python_shebang_for = [ + 'src/*/*.py', + 'src/*/*/*.py', + 'src/*/*/*/*.py', +] + +local_scripts = [ + 'createPeakMatrix.sh', + 'createDataset.sh', + 'deconvolution.sh', + 'trainModel.sh', + 'validation.sh', +] + +postinstallcmds = [ + "sed -i 's|python |python %(installdir)s/|g' %(installdir)s/*.sh" +] + ['chmod a+rx %%(installdir)s/%s' % script for script in local_scripts] + +sanity_check_paths = { + 'files': local_scripts, + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%s --help | grep '^Usage:'" % script for script in local_scripts] + +moduleclass = 'bio' From 5fa5548358f6149cc23dc86f519dd290734ff659 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 11 Oct 2024 16:20:55 +0200 Subject: [PATCH 129/524] Delete easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb --- .../tensorstore-0.1.53-foss-2023a.eb | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb deleted file mode 100644 index 0637b6107cb..00000000000 --- a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb +++ /dev/null @@ -1,62 +0,0 @@ -# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/02 -easyblock = 'PythonBundle' - -name = 'tensorstore' -version = '0.1.53' - -homepage = 'https://github.com/google/tensorstore' -description = """TensorStore is an open-source C++ and Python software library designed for -storage and manipulation of large multi-dimensional arrays.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [ - ('NASM', '2.16.01'), - ('pybind11', '2.11.1'), - ('Bazel', '6.3.1'), - - - - ('PyYAML', '6.0'), - ('zlib', '1.2.13'), - ('LibTIFF', '4.5.0'), - ('snappy', '1.1.10'), - ('Brotli', '1.0.9'), - ('protobuf', '24.0'), - ('bzip2', '1.0.8'), - ('zstd', '1.5.5'), - ('libwebp', '1.3.1'), - ('nlohmann_json', '3.11.2'), - ('Blosc', '1.21.5'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('ml_dtypes', '0.3.2'), -] - -use_pip = True - - -local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" -local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" -local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? -local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" -local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" -# inject CFLAGS: -local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" - - -local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp - -exts_list = [ - (name, version, { - 'installopts': '-v', - 'preinstallopts': local_ts_preinstall, - 'checksums': ['45ef74b2dc9f2cd5f766bc373ded91d681cd021cc69d16592df48abaeb81af56'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From 9da4bac990ba8eb5a2388875d10d7816797e6dc3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 11 Oct 2024 16:21:27 +0200 Subject: [PATCH 130/524] Delete easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch --- ...a-dep-paths-shebang-UniRef30_2023_02.patch | 175 ------------------ 1 file changed, 175 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch deleted file mode 100644 index c84bb7710d6..00000000000 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30_2023_02.patch +++ /dev/null @@ -1,175 +0,0 @@ -pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data -(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); -pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild -author: Kenneth Hoste (HPC-UGent) -update 2.0.1 -> 2.1.0/2.1.2/2.3.0/2.3.2: Thomas Hoffmann (EMBL); -update to uniref30 2023.02 (THEMBL) - -diff -ru alphafold-2.3.2/run_alphafold.py alphafold-2.3.2_data-dep-paths/run_alphafold.py ---- alphafold-2.3.2/run_alphafold.py 2023-03-27 13:50:49.000000000 +0200 -+++ alphafold-2.3.2_data-dep-paths/run_alphafold.py 2023-04-06 09:59:41.304466108 +0200 -@@ -1,3 +1,4 @@ -+#!/usr/bin/env python - # Copyright 2021 DeepMind Technologies Limited - # - # Licensed under the Apache License, Version 2.0 (the "License"); -@@ -42,6 +43,46 @@ - import numpy as np - - # Internal import (7716). -+use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) -+use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) -+ -+data_dir = os.getenv('ALPHAFOLD_DATA_DIR') -+use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' -+ -+if data_dir: -+ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') -+ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') -+ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') -+ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') -+ if use_monomer_preset: -+ pdb_seqres_database_path = None -+ uniprot_database_path = None -+ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') -+ else: -+ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') -+ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') -+ pdb70_database_path = None -+ if use_reduced_dbs: -+ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') -+ uniref30_database_path = None -+ bfd_database_path = None -+ else: -+ small_bfd_database_path = None -+ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') -+ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2023_02') -+else: -+ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") -+ uniref90_database_path = None -+ mgnify_database_path = None -+ bfd_database_path = None -+ uniref30_database_path = None -+ pdb70_database_path = None -+ template_mmcif_dir = None -+ obsolete_pdbs_path = None -+ small_bfd_database_path = None -+ uniprot_database_path = None -+ pdb_seqres_database_path = None -+ use_gpu_relax = None - - logging.set_verbosity(logging.INFO) - -@@ -59,7 +100,7 @@ - 'separated by commas. All FASTA paths must have a unique basename as the ' - 'basename is used to name the output directories for each prediction.') - --flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') -+flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') - flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' - 'store the results.') - flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), -@@ -71,32 +112,32 @@ - flags.DEFINE_string('hmmsearch_binary_path', shutil.which('hmmsearch'), - 'Path to the hmmsearch executable.') - flags.DEFINE_string('hmmbuild_binary_path', shutil.which('hmmbuild'), -- 'Path to the hmmbuild executable.') -+ 'Path to the hmmbuild executable.') - flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), -- 'Path to the Kalign executable.') --flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' -- 'database for use by JackHMMER.') --flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' -- 'database for use by JackHMMER.') --flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' -- 'database for use by HHblits.') --flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' -- 'version of BFD used with the "reduced_dbs" preset.') --flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' -- 'database for use by HHblits.') --flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' -- 'database for use by JackHMMer.') --flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' -- 'database for use by HHsearch.') --flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' -- 'seqres database for use by hmmsearch.') --flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' -- 'template mmCIF structures, each named .cif') -+ 'Path to the Kalign executable.') -+flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' -+ 'database for use by JackHMMER.') -+flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' -+ 'database for use by JackHMMER.') -+flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' -+ 'database for use by HHblits.') -+flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' -+ 'version of BFD used with the "reduced_dbs" preset.') -+flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' -+ 'database for use by HHblits.') -+flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' -+ 'database for use by JackHMMer.') -+flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' -+ 'database for use by HHsearch.') -+flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' -+ 'seqres database for use by hmmsearch.') -+flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' -+ 'template mmCIF structures, each named .cif') - flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' -- 'to consider. Important if folding historical test sets.') --flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' -- 'mapping from obsolete PDB IDs to the PDB IDs of their ' -- 'replacements.') -+ 'to consider. Important if folding historical test sets.') -+flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' -+ 'mapping from obsolete PDB IDs to the PDB IDs of their ' -+ 'replacements.') - flags.DEFINE_enum('db_preset', 'full_dbs', - ['full_dbs', 'reduced_dbs'], - 'Choose preset MSA database configuration - ' -@@ -137,7 +178,7 @@ - 'distracting stereochemical violations but might help ' - 'in case you are having issues with the relaxation ' - 'stage.') --flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' -+flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' - 'Relax on GPU can be much faster than CPU, so it is ' - 'recommended to enable if possible. GPUs must be available' - ' if this setting is enabled.') -@@ -334,6 +375,10 @@ - 'sure it is installed on your system.') - - use_small_bfd = FLAGS.db_preset == 'reduced_dbs' -+ if use_small_bfd and data_dir: -+ bfd_database_path = None -+ uniref30_database_path = None -+ - _check_flag('small_bfd_database_path', 'db_preset', - should_be_set=use_small_bfd) - _check_flag('bfd_database_path', 'db_preset', -@@ -456,13 +501,7 @@ - flags.mark_flags_as_required([ - 'fasta_paths', - 'output_dir', -- 'data_dir', -- 'uniref90_database_path', -- 'mgnify_database_path', -- 'template_mmcif_dir', - 'max_template_date', -- 'obsolete_pdbs_path', -- 'use_gpu_relax', - ]) - - app.run(main) -diff -ru alphafold-2.3.2/scripts/download_uniref30.sh alphafold-2.3.2_uniref30/scripts/download_uniref30.sh ---- alphafold-2.3.2/scripts/download_uniref30.sh 2023-03-27 13:50:49.000000000 +0200 -+++ alphafold-2.3.2_uniref30/scripts/download_uniref30.sh 2024-02-19 14:41:57.295409862 +0100 -@@ -33,7 +33,8 @@ - ROOT_DIR="${DOWNLOAD_DIR}/uniref30" - # Mirror of: - # https://wwwuser.gwdg.de/~compbiol/uniclust/2021_03/UniRef30_2021_03.tar.gz --SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz" -+#SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz" -+SOURCE_URL="https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz" - BASENAME=$(basename "${SOURCE_URL}") - - mkdir --parents "${ROOT_DIR}" From f8644616b482936c7f85b2a6e8ffb8df0672a932 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 11 Oct 2024 16:53:59 +0200 Subject: [PATCH 131/524] adding easyconfigs: FLANN-1.9.2-foss-2023a.eb, PCL-1.14.1-foss-2023a.eb, treeseg-0.2.2-foss-2023a.eb and patches: treeseg-0.2.2_fix_boost_include.patch --- .../f/FLANN/FLANN-1.9.2-foss-2023a.eb | 40 +++++++++++++ .../p/PCL/PCL-1.14.1-foss-2023a.eb | 32 ++++++++++ .../t/treeseg/treeseg-0.2.2-foss-2023a.eb | 48 +++++++++++++++ .../treeseg-0.2.2_fix_boost_include.patch | 58 +++++++++++++++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb new file mode 100644 index 00000000000..37143785fe1 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb @@ -0,0 +1,40 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.9.2' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e26829bb0017f317d9cc45ab83ddcb8b16d75ada1ae07157006c1e7d601c8824'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lz4', '1.9.4'), +] + +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], +} + +sanity_check_commands = ["python -c 'import pyflann'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb b/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb new file mode 100644 index 00000000000..97f57817025 --- /dev/null +++ b/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'PCL' +version = '1.14.1' + +homepage = 'https://pointclouds.org/' +description = """The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and + point cloud processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5dc5e09509644f703de9a3fb76d99ab2cc67ef53eaf5637db2c6c8b933b28af6'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost', '1.82.0'), + ('Eigen', '3.4.0'), + ('FLANN', '1.9.2'), + ('VTK', '9.3.0'), + ('Qhull', '2020.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb new file mode 100644 index 00000000000..27d7480c372 --- /dev/null +++ b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'treeseg' +version = '0.2.2' + +homepage = 'https://github.com/apburt/treeseg' +description = """ +treeseg has been developed to near-automatically segment individual tree point +clouds from high-density larger-area lidar point clouds acquired in forests. A +formal, albeit somewhat outdated description of the methods can be found in our +paper (https://doi.org/10.1111/2041-210X.13121).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/apburt/treeseg/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_boost_include.patch'] +checksums = [ + {'v0.2.2.tar.gz': '69d674ff5eafb24af5a5166fa3ed3b00ebafe9540e747f24a209bb5be3c5227c'}, + {'treeseg-0.2.2_fix_boost_include.patch': '5bc6704c07f61dc24255397327906ed7c2ccc95b2518b51d8b2c2089b746759f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('PCL', '1.14.1'), + ('Armadillo', '12.6.2'), +] + +_libs = ['libleafsep.%s' % SHLIB_EXT, 'libtreeseg.%s' % SHLIB_EXT] + +_bins = ['downsample', 'getcrownvolume', 'nearestneighbour', 'pcdPointXYZRGB2txt', 'segmentcrown', 'sepwoodleaf', + 'txtPointTreeseg2pcd', 'findstems', 'getdtmslice', 'pcdPointTreeseg2txt', 'plotcoords', 'segmentstem', 'thin'] + +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/{lib,bin}', + 'cp %s %%(installdir)s/lib/' % ' '.join(_libs), + 'cp %s %%(installdir)s/bin/' % ' '.join(_bins), +]) + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + ['lib/%s' % x for x in _libs], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch new file mode 100644 index 00000000000..baedd0de22f --- /dev/null +++ b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch @@ -0,0 +1,58 @@ +From cc6ff5b3b53a227c34171ea91164f4eaa035c890 Mon Sep 17 00:00:00 2001 +From: david +Date: Mon, 20 Mar 2023 21:22:20 +0100 +Subject: [PATCH] fix make error: split is not a member of boost + +--- + src/pcdPointTreeseg2txt.cpp | 1 + + src/pcdPointXYZRGB2txt.cpp | 1 + + src/treeseg.cpp | 1 + + src/txtPointTreeseg2pcd.cpp | 1 + + 4 files changed, 4 insertions(+) + +diff --git a/src/pcdPointTreeseg2txt.cpp b/src/pcdPointTreeseg2txt.cpp +index b189e55..af4d865 100644 +--- a/src/pcdPointTreeseg2txt.cpp ++++ b/src/pcdPointTreeseg2txt.cpp +@@ -1,6 +1,7 @@ + #include "treeseg.h" + + #include ++#include + + int main (int argc, char **argv) + { +diff --git a/src/pcdPointXYZRGB2txt.cpp b/src/pcdPointXYZRGB2txt.cpp +index 9fd1520..f99458f 100644 +--- a/src/pcdPointXYZRGB2txt.cpp ++++ b/src/pcdPointXYZRGB2txt.cpp +@@ -1,4 +1,5 @@ + #include ++#include + + int main (int argc, char **argv) + { +diff --git a/src/treeseg.cpp b/src/treeseg.cpp +index a7a0fd3..590759e 100644 +--- a/src/treeseg.cpp ++++ b/src/treeseg.cpp +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + + //File IO + +diff --git a/src/txtPointTreeseg2pcd.cpp b/src/txtPointTreeseg2pcd.cpp +index cf8b2a0..04abfbe 100644 +--- a/src/txtPointTreeseg2pcd.cpp ++++ b/src/txtPointTreeseg2pcd.cpp +@@ -1,6 +1,7 @@ + #include "treeseg.h" + + #include ++#include + + int main (int argc, char **argv) + { From d477d9cf8f8d8005994ad356f93568010bf2cfe1 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 11 Oct 2024 18:25:22 +0200 Subject: [PATCH 132/524] Update easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb index c8b2b71819c..d75527cdfb0 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ sanity_check_paths = { - 'files': ['lib/libtbb.so', 'lib/libtbbmalloc.so'], + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], 'dirs': ['lib', 'include', 'share'], } From 5ac6d9b8705b95306e25b7e954cf155be5b40699 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 11 Oct 2024 18:42:23 +0200 Subject: [PATCH 133/524] patch requirements --- .../c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb index 4f21285268a..229fbc757ee 100644 --- a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -104,6 +104,8 @@ exts_list = [ 'checksums': ['76e67490231acef7f70cf36ab129df72fb2b0256dada7051001ab3b9f8699bf4'], }), ('asteroid', '0.7.0', { + # requirement too strict + 'preinstallopts': "sed -i 's/torchmetrics<=0.11.4/torchmetrics/g' setup.py && ", 'checksums': ['0326f28c5342495cb08ba0520efd0e21e39435dfd78854837fdd5a6c9c9ca410'], }), ('everett', '3.1.0', { From c81b3e5f64554bb786e677b1215697bcd979ed36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Oct 2024 19:52:18 +0200 Subject: [PATCH 134/524] use standalone dependency for Optax 0.2.2 as dependency for dm-haiku 0.0.12 --- .../AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb | 4 ++-- .../dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb | 14 +------------- 2 files changed, 3 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb index 85fd26e21f7..3fe9e6719f6 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -60,7 +60,7 @@ use_pip = True exts_list = [ ('PDBFixer', '1.9', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], }), ('tabulate', '0.9.0', { @@ -93,7 +93,7 @@ exts_list = [ 'AlphaFold-2.3.2_BioPythonPDBData.patch', ], 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': [ {'AlphaFold-2.3.2.tar.gz': '4ea8005ba1b573fa1585e4c29b7d188c5cbfa59b4e4761c9f0c15c9db9584a8e'}, {'AlphaFold-2.0.0_fix-packages.patch': '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db'}, diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb index e5ef56de773..f66f10ec557 100644 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb @@ -19,13 +19,10 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('tensorstore', '0.1.65'), ('protobuf-python', '4.24.0'), + ('Optax', '0.2.2', versionsuffix), ] use_pip = True -# flax > 0.8.5 req jax >= 0.4.27 -# optax 0.2.3 req. jax >= 0.4.27 -# orbax_checkpoint 0.5.18 req. jax >=0.4.25 -# orbax_checkpoint 0.5.19 req. jax >=0.4.26 exts_list = [ ('jmp', '0.0.4', { @@ -34,12 +31,6 @@ exts_list = [ ('flax', '0.8.4', { 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], }), - ('optax', '0.2.2', { - 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], - }), - ('chex', '0.1.86', { - 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], - }), ('nest_asyncio', '1.6.0', { 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], }), @@ -48,9 +39,6 @@ exts_list = [ 'preinstallopts': """sed -i 's/jax >= 0.4.25/&\\*/g' pyproject.toml &&""", 'checksums': ['29f5d311b412760bd6a2fecab3bdbf75407bc00dc6d0457d19478258ecc8fa6d'], }), - ('toolz', '1.0.0', { - 'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'], - }), (name, version, { 'modulename': 'haiku', 'checksums': ['ba0b3acf71433156737fe342c486da11727e5e6c9e054245f4f9b8f0b53eb608'], From d0946917fa07da55a5d802b76ec014d61a5cd143 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sun, 13 Oct 2024 22:50:55 +0200 Subject: [PATCH 135/524] {devel}[system/system,GCCcore/14.2.0] Add pkgconf 2.3.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb | 31 +++++++++++++++++ .../easyconfigs/p/pkgconf/pkgconf-2.3.0.eb | 33 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..de13aa5fb33 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.3.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a2df680578e85f609f2fa67bd3d0fc0dc71b4bf084fc49119de84cd6ed28e723'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb new file mode 100644 index 00000000000..c90cecda0a1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.3.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = SYSTEM + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a2df680578e85f609f2fa67bd3d0fc0dc71b4bf084fc49119de84cd6ed28e723'] + +# add pkgconfig directories in the system to list of default search paths +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -xdev -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +configopts = '--with-pkg-config-dir="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 673f660c31b2b297cd21b91fb21d49455ec523d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sun, 13 Oct 2024 22:51:41 +0200 Subject: [PATCH 136/524] {tools}[GCCcore/14.2.0] Add XZ 5.6.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..388a4bb239c --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.6.3' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a95a49147b2dbb5487517acc0adcd77f9c2032cf00664eeae352405357d14a6c'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.22.5', '', SYSTEM), + ('binutils', '2.42'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From b2f1f2cf7d958c8ace0821770efa4d1fa5b5c31d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sun, 13 Oct 2024 22:52:18 +0200 Subject: [PATCH 137/524] {devel}[GCCcore/14.2.0] Add ncurses 6.5 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..a7ad6d943b2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.5' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['136d91bc269a9a5785e5f9e980bc76ab57428f604ce3e5a5a90cebc767971cc6'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.3.0'), +] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +local_common_configopts += "--enable-pc-files --with-pkg-config-libdir=%(installdir)s/lib/pkgconfig " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts + "--disable-widec", + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] +_pc_names = ['form', 'menu', 'ncurses++', 'ncurses', 'panel'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix] + + ['lib/pkgconfig/%s%s.pc' % (x, y) for x in _pc_names for y in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' From 18fd25a75a24418b566d08bd5f204ae8813e099c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sun, 13 Oct 2024 22:52:43 +0200 Subject: [PATCH 138/524] {lib}[GCCcore/14.2.0] Add libxml 2.13.4 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..5b194eb5a3b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.13.4' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['65d042e1c8010243e617efb02afda20b85c2160acdbfbcb5b26b80cec6515650'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('XZ', '5.6.3'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lib' From 269bca6a6747711e17ed9f44d739a8ace819a8dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sun, 13 Oct 2024 22:53:06 +0200 Subject: [PATCH 139/524] {compiler}[GCCcore/14.2.0] Add AOCC 5.0.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..36d359a6469 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '5.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://download.amd.com/developer/eula/aocc/aocc-5-0/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['966fac2d2c759e9de6e969c10ada7a7b306c113f7f1e07ea376829ec86380daa'] + +clangversion = '17.0.6' + +dependencies = [ + ('binutils', '2.42'), + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('libxml2', '2.13.4'), +] + +moduleclass = 'compiler' From 67633ea97aa1ad162ea5fb70122460d200a136bf Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 08:37:40 +0000 Subject: [PATCH 140/524] add ec for lime --- easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb | 25 ++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb new file mode 100644 index 00000000000..7de4f3e7274 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +configopts = "--prefix %(installdir)s" +buildopts = "all" + +moduleclass = 'phys' \ No newline at end of file From ddb42ab7ab79b5bf091b22fa58e260083937adbc Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 08:39:55 +0000 Subject: [PATCH 141/524] move to GCCcore --- .../l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7de4f3e7274 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +configopts = "--prefix %(installdir)s" +buildopts = "all" + +moduleclass = 'phys' \ No newline at end of file From 5a93edecf9e387a610c9cd1bd28c8c0023fb7174 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 08:48:16 +0000 Subject: [PATCH 142/524] del file with wrong name --- easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb | 25 ---------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb deleted file mode 100644 index 7de4f3e7274..00000000000 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "LIME" -version = "1.3.2" - -homepage = "http://usqcd-software.github.io/c-lime/" -description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, -Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII -and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME -(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, -making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated -with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the -familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, -writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] - -configopts = "--prefix %(installdir)s" -buildopts = "all" - -moduleclass = 'phys' \ No newline at end of file From 733a13f9e274d763b761742198cd6e4e29d529c0 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 08:56:37 +0000 Subject: [PATCH 143/524] correct toolchain --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 7de4f3e7274..5e200e4f66d 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -13,7 +13,7 @@ with Unix files. They are identified only by a record-type (LIME type) character familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCELOWER_TAR_GZ] From 66456e808a330ecf598b4f13dbd63fef58526448 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 09:26:51 +0000 Subject: [PATCH 144/524] lint --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 5e200e4f66d..0857c916e5d 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -4,8 +4,8 @@ name = "LIME" version = "1.3.2" homepage = "http://usqcd-software.github.io/c-lime/" -description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, -Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME (Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated From 1bab3439b3f28e9ad22fdf6010b04f78a2707228 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 09:59:50 +0000 Subject: [PATCH 145/524] add sanity check paths --- .../l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 0857c916e5d..89ac1f9c9e1 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -22,4 +22,33 @@ source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] configopts = "--prefix %(installdir)s" buildopts = "all" +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [ + "bin", + "include", + "lib", + "lib64" + ], +} + moduleclass = 'phys' \ No newline at end of file From 080b9bf906a674d4d11c2666cfbbdcb77af4ce5f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 14 Oct 2024 12:36:14 +0200 Subject: [PATCH 146/524] adding easyconfigs: Rust-1.81.0-GCCcore-13.3.0.eb --- .../r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ca97c690c02 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.81.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.81.0-src.tar.gz': '872448febdff32e50c3c90a7e15f9bb2db131d13c588fe9071b0ed88837ccfa7'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' From 696caa417ab968228eb85baa28ce56e93add0703 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 11:44:05 +0000 Subject: [PATCH 147/524] lint 2 --- .../l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 50 +++++++++---------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 89ac1f9c9e1..80f487c3f05 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -24,31 +24,31 @@ buildopts = "all" sanity_check_paths = { 'files': [ - "bin/lime_pack", - "bin/lime_unpack", - "bin/lime_contents", - "bin/lime_extract_record", - "bin/lime_extract_type", - "lib/liblime.a", - "include/dcap-overload.h", - "include/lime_binary_header.h", - "include/lime_config.h", - "include/lime_config_internal.h", - "include/lime_defs.h", - "include/lime_fixed_types.h", - "include/lime_fseeko.h", - "include/lime.h", - "include/lime_header.h", - "include/lime_reader.h", - "include/lime_utils.h", - "include/lime_writer.h", - ], + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], 'dirs': [ - "bin", - "include", - "lib", - "lib64" - ], + "bin", + "include", + "lib", + "lib64" + ], } -moduleclass = 'phys' \ No newline at end of file +moduleclass = 'phys' From e749be44aa72b5242592b1210259a8308748f24d Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 14 Oct 2024 20:56:25 +0000 Subject: [PATCH 148/524] lint 3 --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 80f487c3f05..17477fe24ec 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -42,13 +42,13 @@ sanity_check_paths = { "include/lime_reader.h", "include/lime_utils.h", "include/lime_writer.h", - ], + ], 'dirs': [ "bin", "include", "lib", "lib64" - ], + ], } moduleclass = 'phys' From dab4d378ac1d05f8e1c6934d6893a0520cbb458b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 14 Oct 2024 23:48:50 +0200 Subject: [PATCH 149/524] Add QCG-PilotJob and dependencies --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb | 25 +++++++ .../p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb | 30 ++++++++ .../plotly.py-5.24.1-GCCcore-13.3.0.eb | 38 ++++++++++ .../tenacity-9.0.0_fix_version.patch | 14 ++++ .../QCG-PilotJob-0.14.1-gfbf-2024a.eb | 70 +++++++++++++++++++ ...trove-classifiers-2024.1.8_fix_setup.patch | 2 + ...ove-classifiers-2024.10.13_fix_setup.patch | 11 +++ .../statsmodels-0.14.4-gfbf-2024a.eb | 35 ++++++++++ .../statsmodels-0.14.4_fix_setup.patch | 13 ++++ 9 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7413eeebb71 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9646f5c0f4d --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '26.2.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.42'), + ('scikit-build-core', '0.10.6'), + ('Cython', '3.0.10'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ZeroMQ', '4.3.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4bccbef4dd8 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.24.1' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True + +exts_list = [ + ('tenacity', '9.0.0', { + 'patches': ['tenacity-9.0.0_fix_version.patch'], + 'checksums': [ + {'tenacity-9.0.0.tar.gz': '807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b'}, + {'tenacity-9.0.0_fix_version.patch': 'e2d65e082569a907b7b8423031c8384bc56552bcf744ae196cb6688014a99837'}, + ], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('plotly', version, { + 'checksums': ['dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch new file mode 100644 index 00000000000..840d0b75f8c --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch @@ -0,0 +1,14 @@ +# What: Putting a manually typed version in setup.cfg, as it wouldnt resolve automatically. +# Author: Denis Kristak (Inuits)diff -ruN tenacity-8.2.3_orig/setup.cfg tenacity-8.2.3/setup.cfg +# Updated for v9.0.0 by maxim-masterov (SURF) +diff -Nru tenacity-9.0.0.orig/setup.cfg tenacity-9.0.0/setup.cfg +--- tenacity-9.0.0.orig/setup.cfg 2024-10-10 16:50:28.669538307 +0200 ++++ tenacity-9.0.0/setup.cfg 2024-10-10 16:50:54.881500726 +0200 +@@ -1,6 +1,7 @@ + [metadata] + name = tenacity + license = Apache 2.0 ++version = 9.0.0 + url = https://github.com/jd/tenacity + summary = Retry code until it succeeds + long_description = Tenacity is a general-purpose retrying library to simplify the task of adding retry behavior to just about anything. diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb new file mode 100644 index 00000000000..86f0119701f --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.14.1' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = "A python service for easy execution of many tasks inside a single allocation." + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('PyZMQ', '26.2.0'), + ('Kaleido', '0.2.1'), + ('statsmodels', '0.14.4'), + ('plotly.py', '5.24.1'), + ('hatchling', '1.24.2'), +] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.48', { + 'checksums': ['d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90'], + }), + ('trove-classifiers', '2024.10.13', { + 'patches': ['trove-classifiers-2024.10.13_fix_setup.patch'], + 'source_tmpl': 'trove_classifiers-2024.10.13.tar.gz', + 'checksums': [ + {'trove_classifiers-2024.10.13.tar.gz': 'b820fc6f9544543afa15e5d9cfc426cde3b20fc2246dff6f019b835731508cef'}, + {'trove-classifiers-2024.10.13_fix_setup.patch': + '1094d951da3b195c71bc109d20601eb611cf3f455c750b3940cbaa9a317dc07a'}, + ], + }), + ('hatch_vcs', '0.4.0', { + 'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'], + }), + ('setuptools-scm', '8.1.0', { + 'source_tmpl': 'setuptools_scm-8.1.0.tar.gz', + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('termcolor', '2.5.0', { + 'checksums': ['998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f'], + }), + ('qcg-pilotjob', version, { + 'modulename': 'qcg.pilotjob', + 'checksums': [ + {'qcg-pilotjob-0.14.1.tar.gz': 'f7e162851dce8d94ee424113bc528bfd0d8cc4668e33a3fd9f058ffce9ef409b'}, + ], + }), + ('qcg-pilotjob-cmds', version, { + 'modulename': 'qcg.pilotjob.cmds', + 'checksums': ['58b2b14a278fc255cad0cec308316242b82cb3a08d6e6a517206af1930b09fe3'], + }), + ('qcg-pilotjob-executor-api', version, { + 'modulename': 'qcg.pilotjob.api', + 'checksums': ['66277105b31d5a6ee3cf87d980ce63298d05f466dd102c2ec65ecdb30545e154'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch index f21ac6f790a..9aa7415c39a 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch @@ -1,3 +1,5 @@ +# What: Put manually typed version in setup.py +# Author: maxim-masterov (SURF) diff -Nru trove-classifiers-2024.1.8-orig/setup.py trove-classifiers-2024.1.8/setup.py --- trove-classifiers-2024.1.8-orig/setup.py 2024-01-08 14:59:52.000000000 +0100 +++ trove-classifiers-2024.1.8/setup.py 2024-01-11 10:37:27.552452000 +0100 diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch new file mode 100644 index 00000000000..d013c7a7115 --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch @@ -0,0 +1,11 @@ +diff -Nru trove_classifiers-2024.10.13.orig/setup.py trove_classifiers-2024.10.13/setup.py +--- trove_classifiers-2024.10.13.orig/setup.py 2024-10-14 23:32:23.824712949 +0200 ++++ trove_classifiers-2024.10.13/setup.py 2024-10-14 23:33:35.655405794 +0200 +@@ -12,6 +12,7 @@ + setup( + name="trove-classifiers", + description="Canonical source for classifiers on PyPI (pypi.org).", ++ version="2024.10.13", + long_description=long_description, + long_description_content_type="text/markdown", + url="https://github.com/pypa/trove-classifiers", diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb new file mode 100644 index 00000000000..ad660eaac79 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.4' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [('Cython', '3.0.10')] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + (name, version, { + 'patches': ['statsmodels-0.14.4_fix_setup.patch'], + 'checksums': [ + {'statsmodels-0.14.4.tar.gz': '5d69e0f39060dc72c067f9bb6e8033b6dccdb0bae101d76a7ef0bcc94e898b67'}, + {'statsmodels-0.14.4_fix_setup.patch': 'f6b0c4b5365700f21a465308ba43ced4a86e695d77dfc54948cc639aa3523b55'}, + ], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch new file mode 100644 index 00000000000..56e9c5f3e2c --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch @@ -0,0 +1,13 @@ +# What: Put manually typed version in setup.py +# Author: maxim-masterov (SURF) +diff -Nru statsmodels-0.14.4.orig/setup.py statsmodels-0.14.4/setup.py +--- statsmodels-0.14.4.orig/setup.py 2024-10-10 16:20:53.020145000 +0200 ++++ statsmodels-0.14.4/setup.py 2024-10-10 16:21:08.330504032 +0200 +@@ -353,6 +353,7 @@ + ext_modules=extensions, + maintainer_email=MAINTAINER_EMAIL, + description=DESCRIPTION, ++ version="0.14.1", + license=LICENSE, + url=URL, + download_url=DOWNLOAD_URL, From 417af737e39af4e32cea71312a2efbaedaf4812f Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 00:37:13 +0200 Subject: [PATCH 150/524] adding easyconfigs: Miniconda3-24.7.1-0.eb --- .../m/Miniconda3/Miniconda3-24.7.1-0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb new file mode 100644 index 00000000000..c70f0086763 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '24.7.1-0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py312_%(version)s-Linux-x86_64.sh'] +checksums = ['33442cd3813df33dcbb4a932b938ee95398be98344dff4c30f7e757cd2110e4f'] + +moduleclass = 'lang' From 7fcd553f41dfeb5dd1b4c31809fedc4cd0fdc0cd Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 00:43:27 +0200 Subject: [PATCH 151/524] adding easyconfigs: XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb --- ...-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb new file mode 100644 index 00000000000..2afd8c1daf8 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.47' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://search.cpan.org/~toddr/XML-Parser-2.46/' +description = "This is a Perl extension interface to James Clark's XML parser, expat." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Perl', '5.38.2'), + ('expat', '2.6.2'), +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML'], +} + +moduleclass = 'data' From 34c885da96b1cf33f4f3686fd6ce7ed8e31f7ba6 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Oct 2024 01:12:35 +0200 Subject: [PATCH 152/524] Fix checksums --- easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb | 1 + .../easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb | 2 +- .../q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb | 2 +- .../easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb index 9646f5c0f4d..05949337114 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['070672c258581c8e4f640b5159297580a9974b026043bd4ab0470be9ed324f1f'] builddependencies = [ ('binutils', '2.42'), diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb index 4bccbef4dd8..86f3008c630 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb @@ -22,7 +22,7 @@ exts_list = [ 'patches': ['tenacity-9.0.0_fix_version.patch'], 'checksums': [ {'tenacity-9.0.0.tar.gz': '807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b'}, - {'tenacity-9.0.0_fix_version.patch': 'e2d65e082569a907b7b8423031c8384bc56552bcf744ae196cb6688014a99837'}, + {'tenacity-9.0.0_fix_version.patch': '7adb47c0a86b6dcfa075a98caa1532f9212f7c6b5f219d205e88b7aa97aa46a0'}, ], }), ('packaging', '24.1', { diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb index 86f0119701f..697c95e3968 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb @@ -36,7 +36,7 @@ exts_list = [ 'checksums': [ {'trove_classifiers-2024.10.13.tar.gz': 'b820fc6f9544543afa15e5d9cfc426cde3b20fc2246dff6f019b835731508cef'}, {'trove-classifiers-2024.10.13_fix_setup.patch': - '1094d951da3b195c71bc109d20601eb611cf3f455c750b3940cbaa9a317dc07a'}, + '50d3ce3edf048bc7496fb3bbee254f13e05bde6b9187e6d098f580df29519a02'}, ], }), ('hatch_vcs', '0.4.0', { diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb index ad660eaac79..ee5cb197a7d 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb @@ -27,7 +27,7 @@ exts_list = [ 'patches': ['statsmodels-0.14.4_fix_setup.patch'], 'checksums': [ {'statsmodels-0.14.4.tar.gz': '5d69e0f39060dc72c067f9bb6e8033b6dccdb0bae101d76a7ef0bcc94e898b67'}, - {'statsmodels-0.14.4_fix_setup.patch': 'f6b0c4b5365700f21a465308ba43ced4a86e695d77dfc54948cc639aa3523b55'}, + {'statsmodels-0.14.4_fix_setup.patch': 'd24bedb6382945ac415927faa9279d75d0a71dad56fce7032a58485981b44fe5'}, ], }), ] From 79d58e031c72e6117c0de0edb7fd072ca7f25358 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Oct 2024 09:27:05 +0200 Subject: [PATCH 153/524] don't hardcode commit ID in sources for NextDenovo, use 'local_commit' local variable --- .../n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb index e22a63378e9..84f6960102e 100644 --- a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb @@ -10,7 +10,7 @@ description = 'NextDenovo is a string graph-based de novo assembler for long rea toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/Nextomics/NextDenovo/archive/'] -sources = [{'download_filename': '0e5fa5d.tar.gz', 'filename': SOURCE_TAR_GZ}] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['bbe43124e7d63cbe33179c2abf2de60797bb7361a7f7a2b5fc33bf62a4479726'] builddependencies = [('binutils', '2.40')] From a9abeb9dc82990c1ac00571bcfd72adcd9020d01 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 15 Oct 2024 07:36:12 +0000 Subject: [PATCH 154/524] add checksum --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 17477fe24ec..63b1b1fb950 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -19,6 +19,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + configopts = "--prefix %(installdir)s" buildopts = "all" From 592ebbe77705b3a2412d7e5e44e3ebe733282094 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 15 Oct 2024 08:30:45 +0000 Subject: [PATCH 155/524] reintroduce build deps --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 63b1b1fb950..d651e57e484 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -15,6 +15,10 @@ writing, and manipulating LIME files and a small set of utilities for examining, toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('GCCcore', '12.3.0'), + ('binutils', '2.40') +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] From 4a2c7c317398742f735e57f17844fe3cdd99bf8c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Oct 2024 10:32:42 +0200 Subject: [PATCH 156/524] Revert changes --- .../q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch index 9aa7415c39a..f21ac6f790a 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch @@ -1,5 +1,3 @@ -# What: Put manually typed version in setup.py -# Author: maxim-masterov (SURF) diff -Nru trove-classifiers-2024.1.8-orig/setup.py trove-classifiers-2024.1.8/setup.py --- trove-classifiers-2024.1.8-orig/setup.py 2024-01-08 14:59:52.000000000 +0100 +++ trove-classifiers-2024.1.8/setup.py 2024-01-11 10:37:27.552452000 +0100 From 745c4f14029d99945bf10f33dac429000acffdb8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Oct 2024 11:02:26 +0200 Subject: [PATCH 157/524] Add comments --- .../q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch index d013c7a7115..b1a4d34af27 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch @@ -1,3 +1,5 @@ +# What: Put manually typed version in setup.py +# Author: maxim-masterov (SURF) diff -Nru trove_classifiers-2024.10.13.orig/setup.py trove_classifiers-2024.10.13/setup.py --- trove_classifiers-2024.10.13.orig/setup.py 2024-10-14 23:32:23.824712949 +0200 +++ trove_classifiers-2024.10.13/setup.py 2024-10-14 23:33:35.655405794 +0200 From 3c21e4d3741db9bda1c890abce308dc480d4b3f1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Oct 2024 11:03:09 +0200 Subject: [PATCH 158/524] Change checksum for the trove-classifiers patch --- .../q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb index 697c95e3968..ae1b1f87ea1 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb @@ -36,7 +36,7 @@ exts_list = [ 'checksums': [ {'trove_classifiers-2024.10.13.tar.gz': 'b820fc6f9544543afa15e5d9cfc426cde3b20fc2246dff6f019b835731508cef'}, {'trove-classifiers-2024.10.13_fix_setup.patch': - '50d3ce3edf048bc7496fb3bbee254f13e05bde6b9187e6d098f580df29519a02'}, + 'c90cace5dd0b8a98c60c68681fe453aea97c99038df21c8ad10e11c6816d84af'}, ], }), ('hatch_vcs', '0.4.0', { From 7b7bf5cafc50d26ccfc91590ee1d5d2fb26f367d Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 11:21:48 +0200 Subject: [PATCH 159/524] adding easyconfigs: MCR-R2024b.eb --- easybuild/easyconfigs/m/MCR/MCR-R2024b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2024b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb new file mode 100644 index 00000000000..17ad8df12f6 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb @@ -0,0 +1,17 @@ +name = 'MCR' +version = 'R2024b' # runtime version 24.2 +local_update = '0' + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['c46f4b55747aa4a8c03c1ece5bd5360c4dbb2ca402608fbd44688ba55f9b7a54'] + +moduleclass = 'math' From 4117819f1fd949e09c626251a6ac8e5f96d598a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 15 Oct 2024 11:55:30 +0200 Subject: [PATCH 160/524] adding easyconfigs: NanoPack-20230602-foss-2023a.eb, kyber-0.4.0-GCC-12.3.0.eb and patches: kyber-0.4.0_requirements.patch --- .../k/kyber/kyber-0.4.0-GCC-12.3.0.eb | 443 +++++++++++++++ .../k/kyber/kyber-0.4.0_requirements.patch | 521 ++++++++++++++++++ .../NanoPack/NanoPack-20230602-foss-2023a.eb | 33 ++ 3 files changed, 997 insertions(+) create mode 100644 easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/k/kyber/kyber-0.4.0_requirements.patch create mode 100644 easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb diff --git a/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..dcc3606d19d --- /dev/null +++ b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,443 @@ +easyblock = 'Cargo' + +name = 'kyber' +version = '0.4.0' + +homepage = 'https://github.com/wdecoster/kyber' +description = """Tool to quickly make a minimalistic 600x600 pixels + heatmap image of read length (log-transformed) and read accuracy.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/kyber/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['kyber-0.4.0_requirements.patch'] +checksums = [ + {'v0.4.0.tar.gz': '1a89538d2795e5f589fd18280de4443d3311454ed70f595b3e6611bd8d8811e1'}, + {'ab_glyph_rasterizer-0.1.8.tar.gz': 'c71b1793ee61086797f5c80b6efa2b8ffa6d5dd703f118545808a7f2e27f7046'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'bio-types-0.13.0.tar.gz': 'dfa990f40a28735fa598dc3dd58d73e62e6b41458959d623903b927ba7b04c80'}, + {'bit_field-0.10.2.tar.gz': 'dc827186963e592360843fb5ba4b973e145841266c1357f7180c43526f2e5b61'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bumpalo-3.12.0.tar.gz': '0d261e256854913907f67ed06efbc3338dfe6179796deefc1ff763fc1aee5535'}, + {'bytemuck-1.13.1.tar.gz': '17febce684fd15d89027105661fec94afb475cb995fbc59d2865198446ba2eea'}, + {'byteorder-1.4.3.tar.gz': '14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610'}, + {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'}, + {'cc-1.0.79.tar.gz': '50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f'}, + {'cfg-if-1.0.0.tar.gz': 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"0.11.0" + source = "registry+https://github.com/rust-lang/crates.io-index" +-checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623" ++checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01" + + [[package]] + name = "strum_macros" +@@ -1468,7 +1676,25 @@ + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0" + dependencies = [ +- "windows-targets", ++ "windows-targets 0.42.2", ++] ++ ++[[package]] ++name = "windows-sys" ++version = "0.48.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9" ++dependencies = [ ++ "windows-targets 0.48.5", ++] ++ ++[[package]] ++name = "windows-sys" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d" ++dependencies = [ ++ "windows-targets 0.52.0", + ] + + [[package]] +@@ -1477,13 +1703,43 @@ + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071" + dependencies = [ +- "windows_aarch64_gnullvm", +- "windows_aarch64_msvc", +- "windows_i686_gnu", +- "windows_i686_msvc", +- "windows_x86_64_gnu", +- "windows_x86_64_gnullvm", +- "windows_x86_64_msvc", ++ "windows_aarch64_gnullvm 0.42.2", ++ "windows_aarch64_msvc 0.42.2", ++ "windows_i686_gnu 0.42.2", ++ "windows_i686_msvc 0.42.2", ++ "windows_x86_64_gnu 0.42.2", ++ "windows_x86_64_gnullvm 0.42.2", ++ "windows_x86_64_msvc 0.42.2", ++] ++ ++[[package]] ++name = "windows-targets" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c" ++dependencies = [ ++ "windows_aarch64_gnullvm 0.48.5", ++ "windows_aarch64_msvc 0.48.5", ++ "windows_i686_gnu 0.48.5", ++ "windows_i686_msvc 0.48.5", ++ "windows_x86_64_gnu 0.48.5", ++ "windows_x86_64_gnullvm 0.48.5", ++ "windows_x86_64_msvc 0.48.5", ++] ++ ++[[package]] ++name = "windows-targets" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd" ++dependencies = [ ++ "windows_aarch64_gnullvm 0.52.0", ++ "windows_aarch64_msvc 0.52.0", ++ "windows_i686_gnu 0.52.0", ++ "windows_i686_msvc 0.52.0", ++ "windows_x86_64_gnu 0.52.0", ++ "windows_x86_64_gnullvm 0.52.0", ++ "windows_x86_64_msvc 0.52.0", + ] + + [[package]] +@@ -1493,42 +1749,126 @@ + checksum = "597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8" + + [[package]] ++name = "windows_aarch64_gnullvm" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" ++ ++[[package]] ++name = "windows_aarch64_gnullvm" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea" ++ ++[[package]] + name = "windows_aarch64_msvc" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43" + + [[package]] ++name = "windows_aarch64_msvc" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc" ++ ++[[package]] ++name = "windows_aarch64_msvc" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef" ++ ++[[package]] + name = "windows_i686_gnu" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f" + + [[package]] ++name = "windows_i686_gnu" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e" ++ ++[[package]] ++name = "windows_i686_gnu" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313" ++ ++[[package]] + name = "windows_i686_msvc" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060" + + [[package]] ++name = "windows_i686_msvc" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406" ++ ++[[package]] ++name = "windows_i686_msvc" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a" ++ ++[[package]] + name = "windows_x86_64_gnu" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36" + + [[package]] ++name = "windows_x86_64_gnu" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e" ++ ++[[package]] ++name = "windows_x86_64_gnu" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd" ++ ++[[package]] + name = "windows_x86_64_gnullvm" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3" + + [[package]] ++name = "windows_x86_64_gnullvm" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc" ++ ++[[package]] ++name = "windows_x86_64_gnullvm" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e" ++ ++[[package]] + name = "windows_x86_64_msvc" + version = "0.42.2" + source = "registry+https://github.com/rust-lang/crates.io-index" + checksum = "9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0" + + [[package]] ++name = "windows_x86_64_msvc" ++version = "0.48.5" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538" ++ ++[[package]] ++name = "windows_x86_64_msvc" ++version = "0.52.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04" ++ ++[[package]] + name = "zune-inflate" + version = "0.2.51" + source = "registry+https://github.com/rust-lang/crates.io-index" diff --git a/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb new file mode 100644 index 00000000000..00ae2ecf8e2 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'NanoPack' +version = '20230602' +local_commit = '4059a0a' + +homepage = 'https://daler.github.io/pybedtools' +description = "Collection of long read processing and analysis tools." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/wdecoster/nanopack/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['b533dd54bf9688a24faf9cb724050ace87bba18b2f469e1116ae47c9ae26cdc1'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoStat', '1.6.0'), + ('NanoFilt', '2.8.0'), + ('NanoLyse', '1.2.1'), + ('NanoPlot', '1.43.0'), + ('NanoComp', '1.24.0'), + ('nanoQC', '0.9.4'), + ('kyber', '0.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 4738f993b7d96bbc7c77a5406a50af1304eb4b29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 15 Oct 2024 12:57:01 +0200 Subject: [PATCH 161/524] add missing checksums --- easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb index dcc3606d19d..14fa1faab67 100644 --- a/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb @@ -192,22 +192,31 @@ checksums = [ {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.45.0.tar.gz': '75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0'}, {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, {'windows-targets-0.52.0.tar.gz': '8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, {'windows_aarch64_gnullvm-0.52.0.tar.gz': 'cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, {'windows_aarch64_msvc-0.52.0.tar.gz': 'bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, {'windows_i686_gnu-0.52.0.tar.gz': 'a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, {'windows_i686_msvc-0.52.0.tar.gz': 'ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, {'windows_x86_64_gnu-0.52.0.tar.gz': '3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, {'windows_x86_64_gnullvm-0.52.0.tar.gz': '1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, {'windows_x86_64_msvc-0.52.0.tar.gz': 'dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04'}, {'zune-inflate-0.2.51.tar.gz': 'a01728b79fb9b7e28a8c11f715e1cd8dc2cda7416a007d66cac55cebb3a8ac6b'}, From 109998f6adcda7efb4174b1e5f73b41ee82d1f13 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 15 Oct 2024 13:32:45 +0200 Subject: [PATCH 162/524] move jedi package from IPython to own EasyConfig --- .../IPython/IPython-8.14.0-GCCcore-12.3.0.eb | 7 +--- .../j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 2 files changed, 35 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb index 78aaf35586a..c43ce71e9a8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), + ('jedi', '0.19.0'), ('ZeroMQ', '4.3.4'), ('lxml', '4.9.2'), ] @@ -58,12 +59,6 @@ exts_list = [ 'modulename': False, 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'] }), - ('parso', '0.8.3', { - 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'] - }), - ('jedi', '0.19.0', { - 'checksums': ['bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4'] - }), ('backcall', '0.2.0', { 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'] }), diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcdb1b6305b --- /dev/null +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'jedi' +version = "0.19.0" + +homepage = 'https://github.com/davidhalter/jedi' +description = """ + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + (name, version, { + 'checksums': ['bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4'], + }), +] + +moduleclass = 'tools' From 180e654467eba3714030cbfee561b33fa46bdaaf Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 15 Oct 2024 12:58:12 +0000 Subject: [PATCH 163/524] no GCCcore dep explicit --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index d651e57e484..92832f43cab 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -16,7 +16,6 @@ writing, and manipulating LIME files and a small set of utilities for examining, toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ - ('GCCcore', '12.3.0'), ('binutils', '2.40') ] From cf5dda8cd0f76c39a027d0c50fb7a3ea3420f70b Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 15 Oct 2024 15:39:07 +0200 Subject: [PATCH 164/524] no explicit prefix Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index 92832f43cab..e1b22b24308 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -24,7 +24,6 @@ source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] -configopts = "--prefix %(installdir)s" buildopts = "all" sanity_check_paths = { From 8b1cac1ee5724279a2f0655678a3fec7ea492957 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 15 Oct 2024 15:39:34 +0200 Subject: [PATCH 165/524] no explicit dir check Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb index e1b22b24308..11dbbfa5025 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -47,12 +47,7 @@ sanity_check_paths = { "include/lime_utils.h", "include/lime_writer.h", ], - 'dirs': [ - "bin", - "include", - "lib", - "lib64" - ], + 'dirs': [], } moduleclass = 'phys' From 2573495123b38a2b1084e56ef018f456824047ed Mon Sep 17 00:00:00 2001 From: lara Date: Tue, 15 Oct 2024 16:36:48 +0200 Subject: [PATCH 166/524] use merged PR 21535 --- easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb index 3d3f419c8ff..5fd72bb4c29 100644 --- a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb @@ -18,7 +18,7 @@ checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] dependencies = [ ('SQLite', '3.42.0'), - ('GMAP-GSNAP', '2024-09-18'), + ('GMAP-GSNAP', '2023-04-20'), ('pblat', '2.5.1'), ('minimap2', '2.26'), ('FASTA', '36.3.8i'), From 0a266f42173f79cff4ac1bfe760e2390fd1820c6 Mon Sep 17 00:00:00 2001 From: lara Date: Tue, 15 Oct 2024 16:39:02 +0200 Subject: [PATCH 167/524] use merged PR 21535 --- .../GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb deleted file mode 100644 index 0a6c4bbf500..00000000000 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-12.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 2016-11-07 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'GMAP-GSNAP' -version = '2024-09-18' - -homepage = 'http://research-pub.gene.com/gmap/' -description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences - GSNAP: Genomic Short-read Nucleotide Alignment Program""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['http://research-pub.gene.com/gmap/src/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['00d28c1a8c95295c8edd006cc0d1b5154cabe185de1f5a5dd8ccdb01fab38a18'] - -# with these deps you can use standard compressed files -# details in http://research-pub.gene.com/gmap/src/README -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), -] - -# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length -# details in http://research-pub.gene.com/gmap/src/README -# configopts = 'MAX_STACK_READLENGTH=300' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['bin/gmap', 'bin/gsnap'], - 'dirs': [], -} - -sanity_check_commands = [ - "gmap --help", - "gsnap --help", -] - -moduleclass = 'bio' From c102c9b0899cc3a02cdd63cd4c0abeedafbb1e78 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 15 Oct 2024 17:08:48 +0200 Subject: [PATCH 168/524] adding easyconfigs: GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb and patches: GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch --- .../GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb | 54 +++++++++++++++++++ ...4-09-18_fix-source-files-for-haswell.patch | 13 +++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb new file mode 100644 index 00000000000..25bc1f03a06 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2024-09-18' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch', +] +checksums = [ + {'gmap-gsnap-2024-09-18.tar.gz': '00d28c1a8c95295c8edd006cc0d1b5154cabe185de1f5a5dd8ccdb01fab38a18'}, + {'GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch': + 'a7ce5bbc83c16d7d4b5f79cf9d96311943fecb114ecab7c6a45e85e95ba54748'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch new file mode 100644 index 00000000000..05112c3e4b5 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch @@ -0,0 +1,13 @@ +Fix source files for Haswell architecture +diff -ru gmap-2024-09-18.orig/src/select64-common.h gmap-2024-09-18/src/select64-common.h +--- gmap-2024-09-18.orig/src/select64-common.h 2023-10-26 02:31:15.000000000 +0200 ++++ gmap-2024-09-18/src/select64-common.h 2024-10-15 16:51:04.695772640 +0200 +@@ -67,7 +67,7 @@ + return place + kSelectInByte[((x >> place) & 0xFF) | (byteRank << 8)]; + #elif defined(__GNUC__) || defined(__clang__) + // GCC and Clang won't inline the intrinsics. +- uint64_t result = uint64_t(1) << k; ++ uint64_t result = (uint64_t)1 << k; + + asm("pdep %1, %0, %0\n\t" + "tzcnt %0, %0" From 21b20daa312fbcf5a70aff52379e11a1045821c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Oct 2024 19:13:17 +0200 Subject: [PATCH 169/524] demote hatchling to build-only dependency in easyconfigs for anndata 0.10.5.post1, Cassiopeia 2.0.0, scanpy 1.9.8, wandb 0.16.1 --- .../easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb | 5 ++++- .../easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb | 2 +- easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb | 5 ++++- easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb | 5 ++++- 4 files changed, 13 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb index b49190c6e5a..8c520bf7d04 100644 --- a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb +++ b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb @@ -9,11 +9,14 @@ description = """anndata is a Python package for handling annotated data matrice toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('h5py', '3.9.0'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb index 69b70834b9b..4de167b9310 100644 --- a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ ('CMake', '3.26.3'), ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), ] dependencies = [ @@ -27,7 +28,6 @@ dependencies = [ ('PyYAML', '6.0'), ('typing-extensions', '4.9.0'), ('tqdm', '4.66.1'), - ('hatchling', '1.18.0'), ('BeautifulSoup', '4.12.2'), ('statsmodels', '0.14.1'), ('Seaborn', '0.13.2'), diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index dc34504eeee..49724e4ae26 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -13,6 +13,10 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'openmp': True} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -25,7 +29,6 @@ dependencies = [ ('networkx', '3.1'), ('numba', '0.58.1'), ('umap-learn', '0.5.5'), - ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), ] diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb index 878f6cc3f72..b8bf8eefb30 100644 --- a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb @@ -9,13 +9,16 @@ tracking your machine learning experiments.""" toolchain = {'name': 'GCC', 'version': '12.3.0'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), ('GitPython', '3.1.40'), ('PyYAML', '6.0'), ('protobuf-python', '4.24.0'), - ('hatchling', '1.18.0'), ] use_pip = True From f7b318e3e20888f191588c4cd8dc0d3e31feca57 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:14:26 +0000 Subject: [PATCH 170/524] adding easyconfigs: redis-py-5.1.1-GCCcore-13.3.0.eb, Redis-7.4.1-GCCcore-13.3.0.eb --- .../r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb | 40 +++++++++++++++++++ .../redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb | 37 +++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..299d66ea0b3 --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.4.1' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bc34b878eb89421bbfca6fa78752343bf37af312a09eb0fae47c9575977dfaa2'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..257c413dbaa --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.1.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('typing-extensions', '4.11.0'), + ('Redis', '7.4.1'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['e1df6dd98eb2bdbc68dabb4b19a5167468ae36dbb53a1c777d5cf7ba8345450e'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" From 8783d3b74251861f398d85d3ea1a9bf1a66d72f9 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:15:24 +0000 Subject: [PATCH 171/524] adding easyconfigs: snappy-1.1.10-GCCcore-13.3.0.eb --- .../s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f72e577513b --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.10' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.1.9_use-default-rtti.patch', +] +checksums = [ + {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' From 87aeb5eea3c5e7791e115603198daa5dae8f03cf Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:16:06 +0000 Subject: [PATCH 172/524] adding easyconfigs: dask-2024.9.1-gfbf-2024a.eb --- .../d/dask/dask-2024.9.1-gfbf-2024a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb b/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb new file mode 100644 index 00000000000..93df8dc002f --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2024.9.1' + +homepage = 'https://dask.org/' +description = """ Dask natively scales Python. Dask provides advanced parallelism for analytics, +enabling performance at scale for the tools you love.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('PyYAML', '6.0.2'), + ('bokeh', '3.6.0'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.2', { + 'checksums': ['d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + (name, version, { + 'checksums': ['06eccc6a68d2882bcd9de24548fa96e8d0da7fbfff0baed3f3c2a526b73dfbb4'], + }), + ('distributed', version, { + 'checksums': ['4d573d89ff4fdde0dd96ad5cfdb843ce8ecef8caf002435bc60d14414dc1e819'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.5', { + 'checksums': ['f6923f9d7ff894b96efbf706118b2cd37fd37751d567e91c22dfd3e2eaa93202'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From 0a0a137c2038f2dbc53285bf3f5d63bc348bef2c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:19:06 +0000 Subject: [PATCH 173/524] adding easyconfigs: mpi4py-4.0.1-gompi-2024a.eb --- .../m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb new file mode 100644 index 00000000000..c3fc1a06dae --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpi4py' +version = '4.0.1' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['f3174b245775d556f4fddb32519a2066ef0592edc810c5b5a59238f9a0a40c89'], + }), +] + +moduleclass = 'lib' From a94b758c13f1d59485cffaef02f501bb39c0a2c1 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:23:21 +0000 Subject: [PATCH 174/524] adding easyconfigs: tornado-6.4.1-GCCcore-13.3.0.eb --- .../t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d4266c8c1c9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.4.1" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "13.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-6.1_increase-default-timeouts.patch'] +checksums = [ + {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, +] + +builddependencies = [ + ("binutils", "2.42"), +] +dependencies = [ + ("Python", "3.12.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" From d30ccb871528923c3dd4efeead2a05b6cfbdcdbd Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:23:46 +0000 Subject: [PATCH 175/524] adding easyconfigs: utf8proc-2.9.0-GCCcore-13.3.0.eb --- .../utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c0a4954721b --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.9.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['18c1626e9fc5a2e192311e36b3010bfc698078f692888940f1fa150547abb0c1'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +separate_build_dir = True + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From bcf1ab811761e4e3c61e6dd40a8df7fd9ca77336 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Oct 2024 20:42:49 +0200 Subject: [PATCH 176/524] add hatch-jupyter-builder build dependency for Cassiopeia --- .../Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb | 7 +--- ...ch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 2 files changed, 36 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb index 4de167b9310..bdcee918b8b 100644 --- a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb @@ -12,6 +12,7 @@ builddependencies = [ ('CMake', '3.26.3'), ('poetry', '1.5.1'), ('hatchling', '1.18.0'), + ('hatch-jupyter-builder', '0.9.1'), ] dependencies = [ @@ -39,12 +40,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('hatch_jupyter_builder', '0.9.1', { - 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], - }), - ('hatch_nodejs_version', '0.3.2', { - 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], - }), ('deprecation', '2.1.0', { 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], }), diff --git a/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..071c33cd4b1 --- /dev/null +++ b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'hatch-jupyter-builder' +version = "0.9.1" + +homepage = 'https://hatch-jupyter-builder.readthedocs.io' +description = """Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is +primarily targeted for package authors who are providing JavaScript as part of +their Python packages. +Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.""" + + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('hatch_nodejs_version', '0.3.2', { + 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], + }), + ('hatch_jupyter_builder', '0.9.1', { + 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], + }), +] + +moduleclass = 'tools' From cbaa2fcc7af602fd1adf69ff0d27ef0cdb9c27ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Oct 2024 20:44:35 +0200 Subject: [PATCH 177/524] demote hatchling to build-only dependency in easyconfigs for phonemizer --- .../easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb index 907228d9281..2569dce3fb5 100644 --- a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb @@ -13,12 +13,15 @@ It is using four backends: espeak, espeak-mbrola, festival and segments. toolchain = {'name': 'gfbf', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), ('eSpeak-NG', '1.51'), ('festival', '2.5.0'), - ('hatchling', '1.18.0'), ('RDFlib', '7.0.0'), ('lxml', '4.9.2'), ] From 7c03a97c82d8cdf907a81ab900fc3d2d98d787a1 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 18:58:19 +0000 Subject: [PATCH 178/524] adding easyconfigs: Ray-project-2.37.0-foss-2024a.eb --- .../Ray-project-2.37.0-foss-2024a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb new file mode 100644 index 00000000000..9b52d2bc91f --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb @@ -0,0 +1,67 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '2.37.0' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('redis-py', '5.1.1'), + ('hatchling', '1.24.2'), + ('Cython', '3.0.10') +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('protobuf-python', '5.28.0'), + ('PyYAML', '6.0.2'), + ('lz4', '1.9.4'), + ('mpi4py', '4.0.1'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.62.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['6c455e008fa86d9e9a9d85bb76da4277c0d7d9668a3bfa70dbe86e9f3c759947'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux2014_%(arch)s.whl', + 'checksums': ['0268c7bc2e8bb6ef9bb8969299deb5857bf672bfcb59da95db7495a8a502f8ba'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' From 96675c98ef08d9444cfeece3117078147ea76fd5 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 19:26:36 +0000 Subject: [PATCH 179/524] adding easyconfigs: modin-0.32.0-foss-2024a.eb --- .../m/modin/modin-0.32.0-foss-2024a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb new file mode 100644 index 00000000000..3a8709cbcfb --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'modin' +version = '0.32.0' + +homepage = 'https://github.com/libvips/pyvips' +description = """This module wraps the libvips image processing library. +libvips is a demand-driven, horizontally threaded image processing library.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('dask', '2024.9.1'), + ('OpenMPI', '5.0.3'), + ('Ray-project', '2.37.0'), + ('Arrow', '17.0.0'), + ('mpi4py', '4.0.1') +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['9f68557add5e92617d006eb98bfd93d298e7d4d9932a0cd48a5e38ee4f30a134'], + }), + ('unidist', '0.7.1', { + 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux_2_17_%(arch)s.manylinux2014_%(arch)s.whl', + 'use_pip_extras': 'mpi', + 'checksums': ['1433753726d8be0e484ca53f75d501afa8c4d94acf9c45a0970949411b4b41e0'], + }), +] + +sanity_check_commands = ['python -c "import modin"'] + +sanity_pip_check = True + +moduleclass = 'tools' From 5b122322f014bc2a659b261c1f1f63781579b068 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 19:32:20 +0000 Subject: [PATCH 180/524] updated description and link --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 3a8709cbcfb..02ac1a15235 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -3,9 +3,8 @@ easyblock = 'PythonBundle' name = 'modin' version = '0.32.0' -homepage = 'https://github.com/libvips/pyvips' -description = """This module wraps the libvips image processing library. -libvips is a demand-driven, horizontally threaded image processing library.""" +homepage = 'https://github.com/modin-project/modin' +description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, scripts, and libraries. """ toolchain = {'name': 'foss', 'version': '2024a'} From 418c24891fc43736ac8ef51ad99faeea1ebe8850 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 19:59:22 +0000 Subject: [PATCH 181/524] adding easyconfigs: bokeh-3.6.0-gfbf-2024a.eb --- .../b/bokeh/bokeh-3.6.0-gfbf-2024a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb new file mode 100644 index 00000000000..fadc3d201b6 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.6.0' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('matplotlib', '3.9.2'), + ('PyYAML', '6.0.2'), + ('Pillow', '10.4.0'), + ('tornado', '6.4.1'), +] + +use_pip = True + +exts_list = [ + ('contourpy', '1.2.1', { + 'checksums': ['4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c'], + }), + ('xyzservices', '2024.4.0', { + 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 96dcf8ff7fd5e3db0d0143fcaa02d110203419b2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 20:10:05 +0000 Subject: [PATCH 182/524] style fixes --- .../a/Arrow/Arrow-17.0.0-gfbf-2024a.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb new file mode 100644 index 00000000000..02154d6671d --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb @@ -0,0 +1,96 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '17.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['9d280d8042e7cf526f8c28d170d93bfab65e50f94569f6a790982a878d8d898d'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Cython', '3.0.10'), + ('Autotools', '20231222'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.2.0'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), # for numpy + ('Boost', '1.85.0'), + ('lz4', '1.9.4'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.6'), + ('snappy', '1.1.10'), + ('RapidJSON', '1.1.0-20240815'), + ('RE2', '2024-03-01'), + ('utf8proc', '2.9.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " + +# install Python bindings +_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " +_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " +_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pyarrow', version, { + 'preinstallopts': ( + "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH" + " && export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s" + " && export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s" + " && export XDG_CACHE_HOME=$TMPDIR && sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml" + " && Python3_ROOT_DIR=$EBROOTPYTHON PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.so" + " ' PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " + ), + 'sources': ['apache-arrow-%(version)s.tar.gz'], + 'start_dir': '%(builddir)s/apache-arrow-%(version)s/python', + 'checksums': ['9d280d8042e7cf526f8c28d170d93bfab65e50f94569f6a790982a878d8d898d'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", +] + +moduleclass = 'data' From 0b077af27564ab150cd806a99f3068d2c42c757c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 20:10:44 +0000 Subject: [PATCH 183/524] adding easyconfigs: RE2-2024-03-01-GCCcore-13.3.0.eb --- .../r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8b5b18c2f51 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = "CMakeMake" + +name = 'RE2' +version = '2024-03-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7b2b3aa8241eac25f674e5b5b2e23d4ac4f0a8891418a2661869f736f03f57f4'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Abseil', '20240722.0'), +] + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From 0549bb87e3ab85c614f5c2fdb0f752e0fe7495b3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Oct 2024 10:08:45 +0200 Subject: [PATCH 184/524] add pyproject-metadata to scikit-build-core v0.9.3 --- .../scikit-build-core-0.9.3-GCCcore-13.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb index 691bd671f50..f95d5d59160 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb @@ -25,6 +25,10 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), ('scikit_build_core', version, { 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], }), From d02928d3218da86571195a19561998c4174a66e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Oct 2024 10:46:19 +0200 Subject: [PATCH 185/524] fix failing RPATH sanity check for recent dorado easyconfigs --- .../dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb | 17 +++++++++++++++++ .../dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb | 19 ++++++++++++++++++- .../dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb | 19 ++++++++++++++++++- 3 files changed, 53 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb index e292bfcc18b..378a9deec6b 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -29,6 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), ] dependencies = [ @@ -70,6 +71,22 @@ configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + sanity_check_paths = { 'files': ['bin/dorado'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb index 0e32e9616ca..9927f0492b4 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -34,6 +34,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), ] dependencies = [ @@ -77,7 +78,23 @@ _copts = [ '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', ] -configopts = ' '.join(_copts) +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] sanity_check_paths = { 'files': ['bin/dorado'], diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb index bf8dbf8c6a8..778c00e0d6e 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb @@ -32,6 +32,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), ] dependencies = [ @@ -76,7 +77,23 @@ _copts = [ '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', ] -configopts = ' '.join(_copts) +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] sanity_check_paths = { 'files': ['bin/dorado'], From 40d24880b97c99c26da4502607ec7a589eccf2c8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 16 Oct 2024 10:50:14 +0200 Subject: [PATCH 186/524] Fix alignment bug in patchelf-0.18.0 by patch --- .../patchelf-0.18.0-GCCcore-12.3.0.eb | 6 +++- .../patchelf-0.18.0_fix-alignment.patch | 31 +++++++++++++++++++ 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb index b87a53d6bda..d213a037191 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch new file mode 100644 index 00000000000..20a233ddc66 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch @@ -0,0 +1,31 @@ +Author - Pavel Tománek +Fix alignment problem when rewriting sections +https://github.com/NixOS/patchelf/pull/566 +--- src/patchelf.cc.orig 2024-10-07 16:45:17.515584318 +0200 ++++ src/patchelf.cc 2024-10-07 16:47:14.622270000 +0200 +@@ -843,7 +843,7 @@ + neededSpace += headerTableSpace; + debug("needed space is %d\n", neededSpace); + +- Elf_Off startOffset = roundUp(fileContents->size(), getPageSize()); ++ Elf_Off startOffset = roundUp(fileContents->size(), alignStartPage); + + // In older version of binutils (2.30), readelf would check if the dynamic + // section segment is strictly smaller than the file (and not same size). +@@ -879,7 +879,7 @@ + rdi(lastSeg.p_type) == PT_LOAD && + rdi(lastSeg.p_flags) == (PF_R | PF_W) && + rdi(lastSeg.p_align) == alignStartPage) { +- auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), getPageSize()); ++ auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), alignStartPage); + if (segEnd == startOffset) { + auto newSz = startOffset + neededSpace - rdi(lastSeg.p_offset); + wri(lastSeg.p_filesz, wri(lastSeg.p_memsz, newSz)); +@@ -898,6 +898,7 @@ + wri(phdr.p_filesz, wri(phdr.p_memsz, neededSpace)); + wri(phdr.p_flags, PF_R | PF_W); + wri(phdr.p_align, alignStartPage); ++ assert(startPage % alignStartPage == startOffset % alignStartPage); + } + + normalizeNoteSegments(); From 439e85f87ae51a5fdab3e53ce2e692121db05e44 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 16 Oct 2024 11:00:47 +0200 Subject: [PATCH 187/524] Ignore user Python packages when running custom sanity check command `pip check` --- easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb | 4 ++-- .../easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb | 4 ++-- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 4 ++-- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb index d4f3285a8fd..b2d0fe9046a 100644 --- a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb @@ -53,7 +53,7 @@ sanity_check_paths = { sanity_check_commands = [ "austin --help", "austin-tui --help", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb index 57a08aeb182..99c52d785fd 100644 --- a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -58,8 +58,8 @@ sanity_check_paths = { sanity_check_commands = [ "gubbins --help", "run_gubbins.py --version", - 'python -c "import gubbins"', - 'python -m pip check', + 'python -s -c "import gubbins"', + 'PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check', ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb index 35889241c08..cf2d0aace66 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb @@ -47,6 +47,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["pip check"] +sanity_check_commands = ["PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check"] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb index 8926a0833fa..42b0118bbe8 100644 --- a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb @@ -47,8 +47,8 @@ sanity_check_paths = { sanity_check_commands = [ "om_mesh_info --help", - "pip check", - "python -c 'import openmeeg'", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", + "python -s -c 'import openmeeg'", ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index 11986d88534..c30243b0d0d 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -92,12 +92,12 @@ sanity_check_paths = { } sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", + "python -s -c 'import PyQt5.QtCore'", "sip5 --help", "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb index 0987fcacdf5..97be3ae2aa6 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb @@ -103,12 +103,12 @@ sanity_check_paths = { } sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", + "python -s -c 'import PyQt5.QtCore'", "sip5 --help", "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = { From 5710105f1b9c20b8158d58ce7d781bf56cddaab7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 16 Oct 2024 11:09:33 +0200 Subject: [PATCH 188/524] Revert changes to patchelf - separated PR created --- .../p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb index d213a037191..b87a53d6bda 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb @@ -10,11 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['patchelf-0.18.0_fix-alignment.patch'] -checksums = [ - {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, - {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, -] +checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] builddependencies = [ ('binutils', '2.40'), From f112ff272a74bbaa158f8557bffed39a475280a0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 16 Oct 2024 11:11:13 +0200 Subject: [PATCH 189/524] Separated PR created for patchelf fix - #21674 --- .../patchelf-0.18.0_fix-alignment.patch | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch deleted file mode 100644 index 20a233ddc66..00000000000 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch +++ /dev/null @@ -1,31 +0,0 @@ -Author - Pavel Tománek -Fix alignment problem when rewriting sections -https://github.com/NixOS/patchelf/pull/566 ---- src/patchelf.cc.orig 2024-10-07 16:45:17.515584318 +0200 -+++ src/patchelf.cc 2024-10-07 16:47:14.622270000 +0200 -@@ -843,7 +843,7 @@ - neededSpace += headerTableSpace; - debug("needed space is %d\n", neededSpace); - -- Elf_Off startOffset = roundUp(fileContents->size(), getPageSize()); -+ Elf_Off startOffset = roundUp(fileContents->size(), alignStartPage); - - // In older version of binutils (2.30), readelf would check if the dynamic - // section segment is strictly smaller than the file (and not same size). -@@ -879,7 +879,7 @@ - rdi(lastSeg.p_type) == PT_LOAD && - rdi(lastSeg.p_flags) == (PF_R | PF_W) && - rdi(lastSeg.p_align) == alignStartPage) { -- auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), getPageSize()); -+ auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), alignStartPage); - if (segEnd == startOffset) { - auto newSz = startOffset + neededSpace - rdi(lastSeg.p_offset); - wri(lastSeg.p_filesz, wri(lastSeg.p_memsz, newSz)); -@@ -898,6 +898,7 @@ - wri(phdr.p_filesz, wri(phdr.p_memsz, neededSpace)); - wri(phdr.p_flags, PF_R | PF_W); - wri(phdr.p_align, alignStartPage); -+ assert(startPage % alignStartPage == startOffset % alignStartPage); - } - - normalizeNoteSegments(); From ccc2f4f080c4911ecaf4dc809c0780c5ca5b9695 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 16 Oct 2024 11:27:33 +0200 Subject: [PATCH 190/524] add patch to GCCcore 13.2.0 and 13.3.0 version of patchelf-0.18.0 --- .../p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb | 6 +++++- .../p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb index 62d26c800db..6dd3411d14b 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb index 9bf25222d44..10b4831c5f7 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.42'), From 2b1f38528066a617e51288929be3669399f685e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 16 Oct 2024 12:19:35 +0200 Subject: [PATCH 191/524] remove `typing-extensions` from `exts_list` --- .../c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb index 229fbc757ee..67df72c221f 100644 --- a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -50,10 +50,6 @@ exts_default_options = { } exts_list = [ - ('typing_extensions', '4.12.2', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d'], - }), ('asteroid_filterbanks', '0.4.0', { 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['4932ac8b6acc6e08fb87cbe8ece84215b5a74eee284fe83acf3540a72a02eaf5'], From dc68a8db0e4363e091147399c1fc75002eb80877 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 16 Oct 2024 11:24:30 +0000 Subject: [PATCH 192/524] adding easyconfigs: phylo-treetime-0.11.4-foss-2023a.eb --- .../phylo-treetime-0.11.4-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb new file mode 100644 index 00000000000..8eaaa826af5 --- /dev/null +++ b/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'phylo-treetime' +version = '0.11.4' + +homepage = 'https://treetime.readthedocs.io/en/latest/index.html' +description = """TreeTime provides routines for ancestral sequence reconstruction and inference of + molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions + of terminal nodes correspond to their sampling times and internal nodes are placed at the most + likely time of divergence. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['f6b1506a58819204b010f5abe36627a127c0efa4cfd5008ea7f25dc0718c0f88'], + 'modulename': 'treetime', + }), +] + +sanity_check_paths = { + 'files': ['bin/treetime'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' From 00b0f0aad6ea650a2ac0f54cc57015c3d836c5f0 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 16 Oct 2024 13:29:50 +0200 Subject: [PATCH 193/524] fix CFLAGS and add sanity check for ParaFly binary --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index ee86c8a1dd6..7e51c59731b 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -18,6 +18,7 @@ sources = [{ 'recursive': True, } }] +patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] checksums = [None] dependencies = [ @@ -25,10 +26,10 @@ dependencies = [ ] # Install ParaFly -postinstallcmds = ["cd %(installdir)s && make"] +postinstallcmds = ["cd %(installdir)s && rm plugins/ParaFly/bin/ParaFly && make"] sanity_check_paths = { - 'files': ['EVidenceModeler'], + 'files': ['EVidenceModeler', 'plugins/ParaFly/bin/ParaFly'], 'dirs': ['plugins/ParaFly', 'testing'], } From b1df92f100a75a9e8bf2b6e1fa8219326b1d4b07 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 16 Oct 2024 13:35:57 +0200 Subject: [PATCH 194/524] remove GCCcore version from PR 21265 --- .../NextPolish-1.4.1-GCCcore-12.3.0.eb | 72 ------------------- 1 file changed, 72 deletions(-) delete mode 100644 easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb deleted file mode 100644 index 857ec88ff80..00000000000 --- a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,72 +0,0 @@ -easyblock = 'MakeCp' - -name = 'NextPolish' -version = '1.4.1' - -homepage = 'https://github.com/Nextomics/NextPolish' -description = 'NextDenovo is a string graph-based de novo assembler for long reads.' - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] -sources = [{ - 'download_filename': 'v%(version)s/%(name)s.tgz', - 'filename': SOURCE_TAR_GZ, -}] -checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] - -builddependencies = [('binutils', '2.40')] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('BWA', '0.7.17'), -] - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, - 'preinstallopts': '', - 'installopts': '', -} - -exts_list = [ - ('Paralleltask', '0.2.3', { - 'modulename': 'paralleltask', - 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], - }), -] - -# fix make -C util - warning: jobserver unavailable -parallel = 1 - -# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 -prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count samtools minimap2/' Makefile && " -prebuildopts += "rm -rf util/bwa && " -prebuildopts += ( - "sed -i" - " -e 's/seq_count bwa_ samtools_/seq_count samtools_/'" - " -e '29d'" # @+make clean -C $(BWADIR) - " -e '18,20d'" # bwa_: @+make -C $(BWADIR) - " -e '1d'" # BWADIR = ./bwa - " util/Makefile && " -) -postinstallcmds = ['cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa'] - -files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] - -sanity_check_paths = { - 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa'], - 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['nextPolish --help'] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'PATH': '', -} - -moduleclass = 'bio' From 69c624d76ea3b6224160f28e05c1cfe72abf21df Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 16 Oct 2024 13:38:12 +0200 Subject: [PATCH 195/524] add patch --- ...odeler-2.0.0_set-correct-CFlags-for-ParaFly.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch new file mode 100644 index 00000000000..eae7fcae4ba --- /dev/null +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch @@ -0,0 +1,12 @@ +diff -ru EVidenceModeler.orig/Makefile EVidenceModeler/Makefile +--- EVidenceModeler.orig/Makefile 2024-10-10 09:25:20.000000000 +0200 ++++ EVidenceModeler/Makefile 2024-10-16 10:58:57.509308850 +0200 +@@ -6,7 +6,7 @@ + CC = gcc + + parafly: +- cd plugins/ParaFly && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install ++ cd plugins/ParaFly && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="$(CFLAGS) -fopenmp" CXXFLAGS="$(CXXFLAGS) -fopenmp" && $(MAKE) install + + + From bd543be93857fad4828a05a5d2b2a719b6e06fff Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 16 Oct 2024 14:56:01 +0200 Subject: [PATCH 196/524] update postinstallcmds to fix RPATH --- .../n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb index 29930bc094a..51a31669463 100644 --- a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb @@ -64,13 +64,14 @@ postinstallcmds = [ # links to binaries "cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa && " "ln -s $EBROOTSAMTOOLS/bin/samtools && ln -s $EBROOTMINIMAP2/bin/minimap2", - # set RPATH to calgs.so - "patchelf --force-rpath --set-rpath '\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib' %(installdir)s/lib/calgs.so", - # set RPATH to nextpolish1.so and nextpolish2.so - "patchelf --force-rpath --set-rpath " - "'\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib' %(installdir)s/lib/nextpolish1.so", - "patchelf --force-rpath --set-rpath " - "'\$ORIGIN:\$ORIGIN/../lib:$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib' %(installdir)s/lib/nextpolish2.so", + # set RPATH to calgs.so, nextpolish1.so and nextpolish2.so + "if %(rpath_enabled)s; then " + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '":$EBROOTZLIB/lib" %(installdir)s/lib/calgs.so && ' + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish1.so && ' + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish2.so; fi', ] files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] From 7106f63160b1418d605882dd02ba151d099300bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Oct 2024 15:03:58 +0200 Subject: [PATCH 197/524] adding easyconfigs: mpl-ascii-0.10.0-gfbf-2023a.eb --- .../mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8381b52dd43 --- /dev/null +++ b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpl-ascii' +version = '0.10.0' + +homepage = 'https://github.com/chriscave/mpl_ascii' +description = "A matplotlib backend that produces plots using only ASCII characters" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'mpl_ascii-%(version)s.tar.gz', + 'checksums': ['8e4ae770d5a612dab0e8055c7677c6c3d271da4f5127cce46a60ce3ce4a4e72c'], + # relax version constraint for rich + 'preinstallopts': """sed -i 's/"rich>=.*"/"rich"/g' pyproject.toml && """, + }), +] + +moduleclass = 'vis' From 8bf07f2fd9bd28c0d915ee922a4ed77eaa4d97bf Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 16 Oct 2024 16:50:06 +0200 Subject: [PATCH 198/524] Update Solids4foam-2.1-foss-2023a.eb - comment install_cmd --- .../easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb index 900ee008508..9c203d21c27 100644 --- a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb @@ -21,8 +21,8 @@ dependencies = [ extract_sources = True +# build + install cmds: install_cmd = 'source $FOAM_BASH && ' -# variables of target install directory install_cmd += 'export WM_PROJECT_USER_DIR=%(installdir)s && ' install_cmd += 'export FOAM_USER_APPBIN=%(installdir)s/bin && ' install_cmd += 'export FOAM_USER_LIBBIN=%(installdir)s/lib && ' From c0c91ba436a2f4af8487fb7b9269f15e72ddfd6a Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 16 Oct 2024 18:18:56 +0200 Subject: [PATCH 199/524] adding easyconfigs: FloPY-3.8.2-gfbf-2023a.eb --- .../f/FloPY/FloPY-3.8.2-gfbf-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb b/easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb new file mode 100644 index 00000000000..7d05748baa4 --- /dev/null +++ b/easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'FloPY' +version = '3.8.2' +homepage = 'https://flopy.readthedocs.io' + +description = "FloPy is a Python package to create, run, and post-process MODFLOW-based models" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +exts_list = [ + ('flopy', version, { + 'checksums': ['0ce2941f4095df2ca1d510f28df57224bdeb90636a3f3beeb199f09f635ddc62'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'geo' From cdf3f667757f6604464c836279296d63e84edebe Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 16 Oct 2024 18:20:27 +0200 Subject: [PATCH 200/524] Fix name --- .../{FloPY-3.8.2-gfbf-2023a.eb => FloPy-3.8.2-gfbf-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/FloPY/{FloPY-3.8.2-gfbf-2023a.eb => FloPy-3.8.2-gfbf-2023a.eb} (97%) diff --git a/easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb b/easybuild/easyconfigs/f/FloPY/FloPy-3.8.2-gfbf-2023a.eb similarity index 97% rename from easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb rename to easybuild/easyconfigs/f/FloPY/FloPy-3.8.2-gfbf-2023a.eb index 7d05748baa4..50f72e07c0d 100644 --- a/easybuild/easyconfigs/f/FloPY/FloPY-3.8.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/f/FloPY/FloPy-3.8.2-gfbf-2023a.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'FloPY' +name = 'FloPy' version = '3.8.2' homepage = 'https://flopy.readthedocs.io' From bfb2f76df4fb81500a2bd4fb80e673a1c1ac52af Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 16 Oct 2024 18:51:20 +0200 Subject: [PATCH 201/524] fix directory name --- .../easyconfigs/f/{FloPY => FloPy}/FloPy-3.8.2-gfbf-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/{FloPY => FloPy}/FloPy-3.8.2-gfbf-2023a.eb (100%) diff --git a/easybuild/easyconfigs/f/FloPY/FloPy-3.8.2-gfbf-2023a.eb b/easybuild/easyconfigs/f/FloPy/FloPy-3.8.2-gfbf-2023a.eb similarity index 100% rename from easybuild/easyconfigs/f/FloPY/FloPy-3.8.2-gfbf-2023a.eb rename to easybuild/easyconfigs/f/FloPy/FloPy-3.8.2-gfbf-2023a.eb From df688f19b10dce9230b6d342dc31afc68e400442 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Oct 2024 19:05:40 +0200 Subject: [PATCH 202/524] adding easyconfigs: Longshot-1.0.0-GCCcore-12.3.0.eb --- .../Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb | 331 ++++++++++++++++++ 1 file changed, 331 insertions(+) create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0a67a58490f --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,331 @@ +easyblock = 'Cargo' + +name = 'Longshot' +version = '1.0.0' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +crates = [ + ('addr2line', '0.24.2'), + ('adler2', '2.0.0'), + ('ahash', '0.7.8'), + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('approx', '0.3.2'), + ('atty', '0.2.14'), + ('autocfg', '1.4.0'), + ('backtrace', '0.3.74'), + ('bio', '0.25.0'), + ('bio-types', '1.0.4'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bumpalo', '3.16.0'), + ('bv', '0.10.0'), + ('bytecount', '0.3.2'), + ('byteorder', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.30'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.38'), + ('clap', '2.34.0'), + ('cmake', '0.1.51'), + ('core-foundation-sys', '0.8.7'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('curl-sys', '0.4.77+curl-8.10.1'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('either', '1.13.0'), + ('error-chain', '0.12.4'), + ('feature-probe', '0.1.1'), + ('fishers_exact', '1.0.1'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('fuchsia-cprng', '0.1.1'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.15'), + ('gimli', '0.31.1'), + ('glob', '0.3.1'), + ('hashbrown', '0.11.2'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('hts-sys', '2.1.4'), + ('iana-time-zone', '0.1.61'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('itertools', '0.7.11'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.72'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.159'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.1.15'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.8.0'), + ('multimap', '0.4.0'), + ('ndarray', '0.12.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.2.4'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.19'), + ('object', '0.36.5'), + ('once_cell', '1.20.2'), + ('openssl-src', '300.3.2+3.3.2'), + ('openssl-sys', '0.9.104'), + ('ordered-float', '1.1.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.31'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.88'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.3.23'), + ('rand', '0.4.6'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rawpointer', '0.1.0'), + ('rdrand', '0.4.0'), + ('regex', '1.11.0'), + ('regex-automata', '0.4.8'), + ('regex-syntax', '0.8.5'), + ('rust-htslib', '0.38.2'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.18'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('shlex', '1.3.0'), + ('statrs', '0.9.0'), + ('strsim', '0.8.0'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('textwrap', '0.11.0'), + ('thiserror', '1.0.64'), + ('thiserror-impl', '1.0.64'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.17'), + ('unicode-ident', '1.0.13'), + ('unicode-normalization', '0.1.24'), + ('unicode-width', '0.1.14'), + ('url', '2.5.2'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.95'), + ('wasm-bindgen-backend', '0.2.95'), + ('wasm-bindgen-macro', '0.2.95'), + ('wasm-bindgen-macro-support', '0.2.95'), + ('wasm-bindgen-shared', '0.2.95'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + 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{'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('Clang', '16.0.6'), + ('Perl', '5.36.1'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 04c550cdc92987b10c86509af0d3d685bba10601 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 16 Oct 2024 19:36:07 +0000 Subject: [PATCH 203/524] newer version --- .../r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..29e697d7f6a --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = "CMakeMake" + +name = 'RE2' +version = '2024-07-02' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7b2b3aa8241eac25f674e5b5b2e23d4ac4f0a8891418a2661869f736f03f57f4'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Abseil', '20240722.0'), +] + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From 21953d9b7b33ec0900ee5f16c11986c46ed29c2e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:36:26 +0200 Subject: [PATCH 204/524] Delete easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb --- .../r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb deleted file mode 100644 index 8b5b18c2f51..00000000000 --- a/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = "CMakeMake" - -name = 'RE2' -version = '2024-03-01' - -homepage = 'https://github.com/google/re2' -description = """ -RE2 is a fast, safe, thread-friendly alternative to backtracking regular -expression engines like those used in PCRE, Perl, and Python. It is a C++ -library. """ - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -toolchainopts = {'pic': True} - -github_account = 'google' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['7b2b3aa8241eac25f674e5b5b2e23d4ac4f0a8891418a2661869f736f03f57f4'] - -builddependencies = [ - ('binutils', '2.42'), - ('CMake', '3.29.3'), -] - -dependencies = [ - ('Abseil', '20240722.0'), -] - -sanity_check_paths = { - 'files': ['lib/libre2.a'], - 'dirs': ['include/re2'], -} - -moduleclass = 'lib' From fa1f4cc3403792cbb701230c75febf0c0891c5d6 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 16 Oct 2024 19:40:33 +0000 Subject: [PATCH 205/524] checksums --- easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb index 29e697d7f6a..3719af682fd 100644 --- a/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb @@ -15,7 +15,7 @@ toolchainopts = {'pic': True} github_account = 'google' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['7b2b3aa8241eac25f674e5b5b2e23d4ac4f0a8891418a2661869f736f03f57f4'] +checksums = ['eb2df807c781601c14a260a507a5bb4509be1ee626024cb45acbd57cb9d4032b'] builddependencies = [ ('binutils', '2.42'), From e65e2d146eac7f86c745b1f427f9ab4bdcd9016e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 00:26:48 +0200 Subject: [PATCH 206/524] Update easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb --- easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb index 02154d6671d..76dcfd2cc40 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb @@ -34,7 +34,7 @@ dependencies = [ ('zstd', '1.5.6'), ('snappy', '1.1.10'), ('RapidJSON', '1.1.0-20240815'), - ('RE2', '2024-03-01'), + ('RE2', '2024-07-02'), ('utf8proc', '2.9.0'), ] From d3c9903f4c049b0ae8945858ea22ecf7f19fc347 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 17 Oct 2024 09:56:09 +0200 Subject: [PATCH 207/524] add sanitychecks --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index 7e51c59731b..57a9cc7c4d6 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -19,7 +19,10 @@ sources = [{ } }] patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] -checksums = [None] +checksums = [ + None, # EVidenceModeler-v2.1.0.tar.gz + '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch +] dependencies = [ ('PASA', '2.5.3',), From df0f3a4b0756716d072bfed484466a00218eb514 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 11:17:40 +0200 Subject: [PATCH 208/524] Update easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 02ac1a15235..268f59942f6 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -4,7 +4,8 @@ name = 'modin' version = '0.32.0' homepage = 'https://github.com/modin-project/modin' -description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, scripts, and libraries. """ +description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, +scripts, and libraries. """ toolchain = {'name': 'foss', 'version': '2024a'} From 5e832007b503a50627985dfb484b038f178225f7 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 17 Oct 2024 09:46:42 +0000 Subject: [PATCH 209/524] more LIME --- .../l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ .../l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb | 53 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cd8ac72a902 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + +buildopts = "all" + +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9bc9d8af551 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + +buildopts = "all" + +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [], +} + +moduleclass = 'phys' From 54533e245231345d4870dc7273f2543e3d5b87f8 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 17 Oct 2024 09:52:04 +0000 Subject: [PATCH 210/524] correct binutil version --- easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb index 9bc9d8af551..d36f23151c8 100644 --- a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb @@ -16,7 +16,7 @@ writing, and manipulating LIME files and a small set of utilities for examining, toolchain = {'name': 'GCCcore', 'version': '13.3.0'} builddependencies = [ - ('binutils', '2.40') + ('binutils', '2.42') ] sources = [SOURCELOWER_TAR_GZ] From d92759e813293b92f334d66afc3a5444c1d9d64f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 17 Oct 2024 12:23:24 +0200 Subject: [PATCH 211/524] add extra paths and make CI happy --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 8 +++++--- easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb | 6 +++++- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index 57a9cc7c4d6..e244792218e 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -20,8 +20,9 @@ sources = [{ }] patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] checksums = [ - None, # EVidenceModeler-v2.1.0.tar.gz - '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch + None, # EVidenceModeler-v2.1.0.tar.gz + '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', + # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch ] dependencies = [ @@ -38,8 +39,9 @@ sanity_check_paths = { modextrapaths = { 'EVM_HOME': '', + 'PATH': '', } -sanity_check_commands = ["$EVM_HOME/EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"] +sanity_check_commands = ["EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb index 5fd72bb4c29..1ee3e15c13f 100644 --- a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb @@ -18,7 +18,7 @@ checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] dependencies = [ ('SQLite', '3.42.0'), - ('GMAP-GSNAP', '2023-04-20'), + ('GMAP-GSNAP', '2024-09-18'), ('pblat', '2.5.1'), ('minimap2', '2.26'), ('FASTA', '36.3.8i'), @@ -48,6 +48,10 @@ sanity_check_paths = { 'dirs': [] } +modextrapaths = { + 'PASAHOME': '', +} + sanity_check_commands = ['command -v %(namelower)s'] moduleclass = 'bio' From 7128e6fb4710f0ba445af85cbd82d4c189252c44 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 17 Oct 2024 12:56:41 +0200 Subject: [PATCH 212/524] make CI happy --- .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index e244792218e..fd353611406 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -21,7 +21,7 @@ sources = [{ patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] checksums = [ None, # EVidenceModeler-v2.1.0.tar.gz - '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', + '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch ] From 37217fb461038262f9146e47cfae5eda56d7fe1b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 17 Oct 2024 13:09:00 +0200 Subject: [PATCH 213/524] Update modin-0.32.0-foss-2024a.eb --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 268f59942f6..ce7cb19ce0d 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -38,8 +38,6 @@ exts_list = [ }), ] -sanity_check_commands = ['python -c "import modin"'] - sanity_pip_check = True moduleclass = 'tools' From 0f5687c1a631d898a13a6f2348cbfbddb47cd0f0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:02:37 +0000 Subject: [PATCH 214/524] adding easyconfigs: hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb, PyZMQ-26.2.0-GCCcore-13.3.0.eb, IPython-8.28.0-GCCcore-13.3.0.eb, jupyter-server-2.14.2-GCCcore-13.3.0.eb, JupyterLab-4.2.5-GCCcore-13.3.0.eb --- ...ch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb | 35 ++++ .../IPython/IPython-8.28.0-GCCcore-13.3.0.eb | 79 ++++++++ .../JupyterLab-4.2.5-GCCcore-13.3.0.eb | 78 ++++++++ .../jupyter-server-2.14.2-GCCcore-13.3.0.eb | 183 ++++++++++++++++++ .../p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb | 29 +++ 5 files changed, 404 insertions(+) create mode 100644 easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.28.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f4483b94edd --- /dev/null +++ b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'hatch-jupyter-builder' +version = "0.9.1" + +homepage = 'https://hatch-jupyter-builder.readthedocs.io' +description = """Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is +primarily targeted for package authors who are providing JavaScript as part of +their Python packages. +Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('hatchling', '1.24.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('hatch_nodejs_version', '0.3.2', { + 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], + }), + ('hatch_jupyter_builder', version, { + 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..163d831276b --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.28.0-GCCcore-13.3.0.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.28.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ZeroMQ', '4.3.5'), + ('lxml', '5.3.0'), + ('jedi', '0.19.1') +] + +sanity_pip_check = True +use_pip = True + +# for the matplotlib-inline required extention we avoid the import sanity check +# as it will fail without matplotlib in the environment, but ipython devs prefer not to make +# matplotlib a required dep (https://github.com/ipython/matplotlib-inline/issues/4) +# we follow the same convention and we not set matplotlib as dependency + +exts_list = [ + ('traitlets', '5.13.0', { + 'checksums': ['9b232b9430c8f57288c1024b34a8f0251ddcc47268927367a0dd3eeaca40deb5'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('executing', '2.0.1', { + 'checksums': ['35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147'], + }), + ('asttokens', '2.4.1', { + 'checksums': ['b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0'], + }), + ('stack_data', '0.6.3', { + 'checksums': ['836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9'], + }), + ('prompt_toolkit', '3.0.41', { + 'checksums': ['941367d97fc815548822aa26c2a269fdc4eb21e9ec05fc5d447cf09bad5d75f0'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('matplotlib-inline', '0.1.6', { + 'modulename': False, + 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['0d0d15ca1e01faeb868ef56bc7ee5a0de5bd66885735682e8a322ae289a13d1a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..abe825dfa69 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.2.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.12.3'), + ('IPython', '8.28.0'), + ('jupyter-server', '2.14.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.25', { + 'checksums': ['548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae'], + }), + ('jupyterlab_server', '2.27.3', { + 'checksums': ['eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4'], + }), + ('jupyter-lsp', '2.2.5', { + 'checksums': ['793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.6', { + 'checksums': ['73f6dbd6eb8c21bbf7ef8efad555481853f5f6acdeaff1edb0694289269ee17f'], + }), + ('httpx', '0.27.2', { + 'checksums': ['f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2'], + }), + ('jupyterlab', version, { + 'checksums': ['ae7f3a1b8cb88b4f55009ce79fa7c06f99d70cd63601ee4aa91815d054f46f75'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-lab', 'bin/jupyter-labextension', 'bin/jupyter-labhub'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f19224e775e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb @@ -0,0 +1,183 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.14.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('maturin', '1.6.0'), # needed by rpds_py + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.12.3'), + ('IPython', '8.28.0'), + ('PyYAML', '6.0.2'), + ('PyZMQ', '26.2.0'), + ('tornado', '6.4.1'), + ('BeautifulSoup', '4.12.3'), # needed by nbconvert +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('terminado', '0.18.1', { + 'checksums': ['de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e'], + }), + ('Send2Trash', '1.8.3', { + 'checksums': ['b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf'], + }), + ('prometheus_client', '0.21.0', { + 'checksums': ['96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e'], + }), + ('overrides', '7.7.0', { + 'checksums': ['55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a'], + }), + ('jupyter_core', '5.7.2', { + 'patches': ['jupyter-core-%(version)s_fix_jupyter_path.patch'], + 'checksums': [ + {'jupyter_core-5.7.2.tar.gz': 'aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'}, + {'jupyter-core-5.7.2_fix_jupyter_path.patch': + '1ed5088728c1ad49687b66e31ed23965c36645ad285693785b2b96c4ff1b2f93'}, + ], + }), + ('fastjsonschema', '2.20.0', { + 'checksums': ['3d48fc5300ee96f5d116f10fe6f28d938e6008f59a6a025c2649475b87f76a23'], + }), + ('tinycss2', '1.3.0', { + 'checksums': ['152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d'], + }), + ('pandocfilters', '1.5.1', { + 'checksums': ['002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e'], + }), + ('mistune', '3.0.2', { + 'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.3.0', { + 'checksums': ['721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.1.0', { + 'checksums': ['0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe'], + }), + ('nbformat', '5.10.4', { + 'checksums': ['322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a'], + }), + ('nbclient', '0.10.0', { + 'checksums': ['4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09'], + }), + ('jupyter_client', '8.6.3', { + 'checksums': ['35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419'], + }), + ('nbconvert', '7.16.4', { + 'checksums': ['86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4'], + }), + ('jupyter_server_terminals', '0.5.3', { + 'checksums': ['5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.20.0', { + 'modulename': 'rpds', + 'checksums': ['d72a210824facfdaf8768cf2d7ca25a042c30320b3020de2fa04640920d4e121'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2024.10.1', { + 'checksums': ['0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272'], + }), + ('jsonschema', '4.23.0', { + 'checksums': ['d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4'], + }), + ('jupyter_events', '0.10.0', { + 'checksums': ['670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('jupyter_server', version, { + 'checksums': ['66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'checksums': ['a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed'], + }), + ('widgetsnbextension', '4.0.13', { + 'checksums': ['ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6'], + }), + ('comm', '0.2.2', { + 'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'], + }), + ('ipywidgets', '8.1.5', { + 'checksums': ['870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17'], + }), + ('notebook_shim', '0.2.4', { + 'checksums': ['b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('ipykernel', '6.29.5', { + 'checksums': ['f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.8.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['57b00de1c8d2c84a61b90880f7e5b6deaf4c312ecbde3a0e8912f2a56c4ac9ae'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f316daeb2f2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '26.2.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['070672c258581c8e4f640b5159297580a9974b026043bd4ab0470be9ed324f1f'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ZeroMQ', '4.3.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' From 2d69a9d5cd2f777489985767c6741ea9b50093fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:16:33 +0000 Subject: [PATCH 215/524] Add jedi --- .../j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b477ad70774 --- /dev/null +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'jedi' +version = "0.19.1" + +homepage = 'https://github.com/davidhalter/jedi' +description = """ + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + (name, version, { + 'checksums': ['cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd'], + }), +] + +moduleclass = 'tools' From 5c2dc204d04266d3d513cc1f4ee481c67e372309 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:18:48 +0000 Subject: [PATCH 216/524] Remove redundant sanity check from jedi easyconfigs --- easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb | 5 ----- easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb | 7 ++----- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb index 5b2a8950603..264d5e60223 100644 --- a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb @@ -29,9 +29,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb index eca3a2e905d..a0891f77c33 100644 --- a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb @@ -6,6 +6,8 @@ version = "0.19.1" homepage = 'https://github.com/davidhalter/jedi' description = """ Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} @@ -29,9 +31,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python3.11/site-packages/jedi'], -} - moduleclass = 'tools' From 3d7355fa47cbf03560a64c7c32ac6e6fecd46056 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:21:18 +0000 Subject: [PATCH 217/524] Fix description --- easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb index 264d5e60223..daf043bb1a5 100644 --- a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb @@ -3,9 +3,11 @@ easyblock = 'PythonBundle' name = 'jedi' version = "0.18.1" -homepage = 'https://jedi.readthedocs.io/en/latest/' +homepage = 'https://github.com/davidhalter/jedi' description = """ - Jedi is a static analysis tool for Python that is typically used in IDEs/editors plugins. + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} From d6a8c94f287138880c37447aadab8b6f2645b234 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:26:57 +0000 Subject: [PATCH 218/524] add scikit-build-core builddep to PyZMQ --- easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb index f316daeb2f2..3d5866c108c 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -14,6 +14,7 @@ checksums = ['070672c258581c8e4f640b5159297580a9974b026043bd4ab0470be9ed324f1f'] builddependencies = [ ('binutils', '2.42'), + ('scikit-build-core', '0.10.6'), ] dependencies = [ ('Python', '3.12.3'), From 82fc3b9ba0f437411383030d18da6748d667c2da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 13:39:31 +0000 Subject: [PATCH 219/524] Add cython builddep to PyZMQ --- easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb index 3d5866c108c..05949337114 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -15,6 +15,7 @@ checksums = ['070672c258581c8e4f640b5159297580a9974b026043bd4ab0470be9ed324f1f'] builddependencies = [ ('binutils', '2.42'), ('scikit-build-core', '0.10.6'), + ('Cython', '3.0.10'), ] dependencies = [ ('Python', '3.12.3'), From 7b2fc969b31836da4d5c1cda759e826fd1b68408 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 14:12:37 +0000 Subject: [PATCH 220/524] adding easyconfigs: aiohttp-3.10.10-GCCcore-13.3.0.eb --- .../aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c13dca7ec6d --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.10.10' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.5', { + 'checksums': ['f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('yarl', '1.12.0', { + 'checksums': ['4c801b9a281a7078e085efbc0e87f0938cea011928c0d48bdcb7c0a58451fb8e'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('aiohappyeyeballs', '2.3.2', { + 'checksums': ['77e15a733090547a1f5369a1287ddfc944bd30df0eb8993f585259c34b405f4e'], + }), + (name, version, { + 'checksums': ['0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From eefc04062c342b658df2530dc8d441b8ceac3ad5 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 14:13:04 +0000 Subject: [PATCH 221/524] adding easyconfigs: boto3-1.35.36-GCCcore-13.3.0.eb --- .../b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..eb03680b8c3 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.35.36' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +exts_list = [ + ('botocore', version, { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.0', { + 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], + }), + (name, version, { + 'checksums': ['586524b623e4fbbebe28b604c6205eb12f263cc4746bccb011562d07e217a4cb'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From fc554d1ca02d9309094319a776e8321816ad4af8 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 14:22:07 +0000 Subject: [PATCH 222/524] adding easyconfigs: s3fs-2024.9.0-foss-2024a.eb --- .../s/s3fs/s3fs-2024.9.0-foss-2024a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb new file mode 100644 index 00000000000..c890c462837 --- /dev/null +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb @@ -0,0 +1,43 @@ +easyblock = "PythonBundle" + +name = 's3fs' +version = '2024.9.0' + +homepage = 'https://github.com/fsspec/s3fs/' +description = """S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3..""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('hatchling', '1.24.2'), + ('aiohttp', '3.10.10'), + ('wrapt', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.35.36', { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.15.2', { + 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], + }), + ('fsspec', version, { + 'checksums': ['4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8'], + }), + (name, version, { + 'checksums': ['6493705abb50374d6b7994f9616d27adbdd8a219c8635100bdc286382efd91f5'], + }), +] + +moduleclass = 'tools' From 0840096cc02a7f811d260229a74166539172381f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 14:38:25 +0000 Subject: [PATCH 223/524] enable some tests --- .../m/modin/modin-0.32.0-foss-2024a.eb | 27 ++++++++++++++----- .../modin-0.32.0_fix-pytest-config.patch | 20 ++++++++++++++ 2 files changed, 40 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index ce7cb19ce0d..63667948103 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'foss', 'version': '2024a'} builddependencies = [ ('Cython', '3.0.10'), + # Needed for tests + ('boto3', '1.35.36'), + ('s3fs', '2024.9.0'), ] dependencies = [ @@ -24,17 +27,27 @@ dependencies = [ ('mpi4py', '4.0.1') ] -download_dep_fail = True use_pip = True +local_pytest_cmd = 'pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py' + exts_list = [ - (name, version, { - 'checksums': ['9f68557add5e92617d006eb98bfd93d298e7d4d9932a0cd48a5e38ee4f30a134'], - }), ('unidist', '0.7.1', { - 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux_2_17_%(arch)s.manylinux2014_%(arch)s.whl', - 'use_pip_extras': 'mpi', - 'checksums': ['1433753726d8be0e484ca53f75d501afa8c4d94acf9c45a0970949411b4b41e0'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], + 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], + }), + (name, version, { + 'patches': ['modin-0.32.0_fix-pytest-config.patch'], + 'runtest': 'MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi %(local_pytest_cmd)s && MODIN_BACKEND=ray %(local_pytest_cmd)s && MODIN_BACKEND=dask %(local_pytest_cmd)s' % {'local_pytest_cmd': local_pytest_cmd}, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], + 'testinstall': True, + 'checksums': [ + {'0.32.0.tar.gz': 'f2ef11f384a7d47eb6680a2f6f4bbc3404fa6290163d36384032daff3837b063'}, + {'modin-0.32.0_fix-pytest-config.patch': + 'c49bd5c072a87321760c7c5eebc957f4f6962763a3526a500fe6330cf3f2b765'}, + ], }), ] diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch new file mode 100644 index 00000000000..990e053d328 --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch @@ -0,0 +1,20 @@ +Removes unnecessary options for pytest that induce additional dependencies. + +--- 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg.orig 2024-10-17 15:56:55.245266649 +0200 ++++ 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg 2024-10-17 15:57:34.748841878 +0200 +@@ -11,15 +11,6 @@ + tag_prefix = + parentdir_prefix = modin- + +-[tool:pytest] +-addopts = --cov-config=setup.cfg --cov=modin --cov-append --cov-report= -m "not exclude_by_default" +-xfail_strict=true +-markers = +- exclude_in_sanity +- exclude_by_default +-filterwarnings = +- error:.*defaulting to pandas.*:UserWarning +- + [isort] + profile = black + From 31fa5b40c6f8a8f7108e7e180025dae5d08de5df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 14:41:14 +0000 Subject: [PATCH 224/524] Add back missing comments --- .../j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb index f19224e775e..e7bc1dceeb0 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb @@ -153,6 +153,8 @@ exts_list = [ ('ipywidgets', '8.1.5', { 'checksums': ['870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17'], }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle ('notebook_shim', '0.2.4', { 'checksums': ['b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb'], }), From e1ee7bb646732fba3b3161b3a483fdae77752388 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:03:31 +0000 Subject: [PATCH 225/524] versions, deps --- easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb index c890c462837..077b8c21b5b 100644 --- a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb @@ -14,6 +14,7 @@ dependencies = [ ('hatchling', '1.24.2'), ('aiohttp', '3.10.10'), ('wrapt', '1.16.0'), + ('boto3', '1.35.36'), ] use_pip = True @@ -26,12 +27,9 @@ exts_list = [ ('botocore', '1.35.36', { 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], }), - ('aioitertools', '0.11.0', { + ('aioitertools', '0.12.0', { 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], }), - ('aiobotocore', '2.15.2', { - 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], - }), ('fsspec', version, { 'checksums': ['4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8'], }), From d8e4f2d2fe0a40765e4c1126f3d4f4b9abb81f98 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:04:13 +0000 Subject: [PATCH 226/524] updated versions --- .../easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb index eb03680b8c3..ed3843de0e9 100644 --- a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb @@ -23,10 +23,13 @@ exts_list = [ ('botocore', version, { 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], }), + ('aiobotocore', '2.15.2', { + 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], + }), ('jmespath', '1.0.1', { 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), - ('s3transfer', '0.10.0', { + ('s3transfer', '0.10.3', { 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], }), (name, version, { From d5d89402c1831f5ad9bcea1e9724f54b7c8a68c3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:05:07 +0000 Subject: [PATCH 227/524] updated deos --- .../easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index c13dca7ec6d..c4a7bff1281 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -23,13 +23,13 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ - ('multidict', '6.0.5', { + ('multidict', '6.1.0', { 'checksums': ['f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da'], }), ('expandvars', '0.12.0', { 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], }), - ('yarl', '1.12.0', { + ('yarl', '1.15.4', { 'checksums': ['4c801b9a281a7078e085efbc0e87f0938cea011928c0d48bdcb7c0a58451fb8e'], }), ('frozenlist', '1.4.1', { @@ -41,7 +41,7 @@ exts_list = [ ('aiosignal', '1.3.1', { 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], }), - ('aiohappyeyeballs', '2.3.2', { + ('aiohappyeyeballs', '2.4.3', { 'checksums': ['77e15a733090547a1f5369a1287ddfc944bd30df0eb8993f585259c34b405f4e'], }), (name, version, { From 94a975f2b6fc5a008d4375f15e24b66addb6ae87 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:05:55 +0000 Subject: [PATCH 228/524] updated hashes --- .../easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index c4a7bff1281..bc4d2eb10da 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -24,13 +24,13 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ ('multidict', '6.1.0', { - 'checksums': ['f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da'], + 'checksums': ['22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a'], }), ('expandvars', '0.12.0', { 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], }), ('yarl', '1.15.4', { - 'checksums': ['4c801b9a281a7078e085efbc0e87f0938cea011928c0d48bdcb7c0a58451fb8e'], + 'checksums': ['a0c5e271058d148d730219ca4f33c5d841c6bd46e05b0da60fea7b516906ccd3'], }), ('frozenlist', '1.4.1', { 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], @@ -42,7 +42,7 @@ exts_list = [ 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], }), ('aiohappyeyeballs', '2.4.3', { - 'checksums': ['77e15a733090547a1f5369a1287ddfc944bd30df0eb8993f585259c34b405f4e'], + 'checksums': ['75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586'], }), (name, version, { 'checksums': ['0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a'], From a582f971ffb0b6d6ca3f60b5ecc7074de0ed1952 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:07:26 +0000 Subject: [PATCH 229/524] hashes --- easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb index 077b8c21b5b..09fd361f0dd 100644 --- a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb @@ -28,7 +28,7 @@ exts_list = [ 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], }), ('aioitertools', '0.12.0', { - 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + 'checksums': ['c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b'], }), ('fsspec', version, { 'checksums': ['4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8'], From 646ab3444003de3d36b3039e25f930f5c05a245d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:17:29 +0000 Subject: [PATCH 230/524] checksums --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 63667948103..209a1027257 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,7 +39,7 @@ exts_list = [ }), (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], - 'runtest': 'MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi %(local_pytest_cmd)s && MODIN_BACKEND=ray %(local_pytest_cmd)s && MODIN_BACKEND=dask %(local_pytest_cmd)s' % {'local_pytest_cmd': local_pytest_cmd}, + 'runtest': "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=ray pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py", 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From 85911e65c2ec3f1d8c290cdad68a7d0447ed1e19 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:22:53 +0000 Subject: [PATCH 231/524] updated deps --- .../easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index bc4d2eb10da..91e8a4ab6fd 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -23,6 +23,9 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ + ('propcache', '0.2.0', { + 'checksums': ['df81779732feb9d01e5d513fad0122efb3d53bbc75f61b2a4f29a020bc985e70'], + }), ('multidict', '6.1.0', { 'checksums': ['22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a'], }), From 552f336802229ede1802a577411caf01169e7e0c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:24:54 +0000 Subject: [PATCH 232/524] updated hashes --- easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb index ed3843de0e9..c1dfd51c463 100644 --- a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb @@ -30,7 +30,7 @@ exts_list = [ 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), ('s3transfer', '0.10.3', { - 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], + 'checksums': ['4f50ed74ab84d474ce614475e0b8d5047ff080810aac5d01ea25231cfc944b0c'], }), (name, version, { 'checksums': ['586524b623e4fbbebe28b604c6205eb12f263cc4746bccb011562d07e217a4cb'], From f8fc45f26835ae4318aff5857a1783d8a124fcbf Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:33:13 +0000 Subject: [PATCH 233/524] remove aiobotocore --- easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb index c1dfd51c463..4f327430573 100644 --- a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb @@ -23,9 +23,6 @@ exts_list = [ ('botocore', version, { 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], }), - ('aiobotocore', '2.15.2', { - 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], - }), ('jmespath', '1.0.1', { 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), From 9af0713a5b68f8104e16492e1ad593ffcfef0a79 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:34:21 +0000 Subject: [PATCH 234/524] updated deps --- .../easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index 91e8a4ab6fd..4a87301f29a 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -23,6 +23,12 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ + ('botocore', '1.35.36', { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), + ('aiobotocore', '2.15.2', { + 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], + }), ('propcache', '0.2.0', { 'checksums': ['df81779732feb9d01e5d513fad0122efb3d53bbc75f61b2a4f29a020bc985e70'], }), From e43b554f2cc14c0bac9c3d0f57143b1c0360b745 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:39:39 +0000 Subject: [PATCH 235/524] updated deps again --- .../a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index 4a87301f29a..a47df7172c4 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -26,18 +26,15 @@ exts_list = [ ('botocore', '1.35.36', { 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], }), - ('aiobotocore', '2.15.2', { - 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], - }), - ('propcache', '0.2.0', { - 'checksums': ['df81779732feb9d01e5d513fad0122efb3d53bbc75f61b2a4f29a020bc985e70'], - }), ('multidict', '6.1.0', { 'checksums': ['22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a'], }), ('expandvars', '0.12.0', { 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], }), + ('propcache', '0.2.0', { + 'checksums': ['df81779732feb9d01e5d513fad0122efb3d53bbc75f61b2a4f29a020bc985e70'], + }), ('yarl', '1.15.4', { 'checksums': ['a0c5e271058d148d730219ca4f33c5d841c6bd46e05b0da60fea7b516906ccd3'], }), @@ -56,6 +53,9 @@ exts_list = [ (name, version, { 'checksums': ['0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a'], }), + ('aiobotocore', '2.15.2', { + 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], + }), ] sanity_pip_check = True From e9f6bded85892f9ddbddb029e1f0af9349f4f81b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 16:25:26 +0000 Subject: [PATCH 236/524] updated deps again --- .../a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index a47df7172c4..adf22b97b48 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -23,8 +23,8 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ - ('botocore', '1.35.36', { - 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), ('multidict', '6.1.0', { 'checksums': ['22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a'], @@ -53,6 +53,12 @@ exts_list = [ (name, version, { 'checksums': ['0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a'], }), + ('aioitertools', '0.12.0', { + 'checksums': ['c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), ('aiobotocore', '2.15.2', { 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], }), From 3ad1d5fb2da28c6b0faeec341ac6326ea8bcc54b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 16:29:47 +0000 Subject: [PATCH 237/524] updated deps again --- .../easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb index adf22b97b48..c6b30e2d82e 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -23,6 +23,9 @@ use_pip = True # aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies exts_list = [ + ('botocore', '1.35.36', { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), ('jmespath', '1.0.1', { 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), From c92315adf558748b15abc046389cba0363f39b92 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 17 Oct 2024 18:41:18 +0200 Subject: [PATCH 238/524] adding easyconfigs: cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb, corrplot-0.95-foss-2023a.eb --- ...sDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb | 34 +++++++++++++++++++ .../c/corrplot/corrplot-0.95-foss-2023a.eb | 28 +++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..d61b8779821 --- /dev/null +++ b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'cisDIVERSITY' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/NarlikarLab/cisDIVERSITY/' +description = """A module discovery tool used for finding diverse sequence architectures, +each one characterized by presence or absence of de novo motifs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/NarlikarLab/cisDIVERSITY/releases/download/v%(version)s/'] +sources = [{ + 'download_filename': '%(name)s_v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['4ba5967fa754ec78b9dd6b6dc9d2ee5de87dbb4d7906d47e57e73aec87897725'] + +dependencies = [ + ('Python', '2.7.18'), + ('numpy', '1.16.6', versionsuffix), + ('corrplot', '0.95'), +] +files_to_copy = [(['learnDiverseModules'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/learnDiverseModules'], + 'dirs': [], +} + +sanity_check_commands = ['learnDiverseModules -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb b/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb new file mode 100644 index 00000000000..ebe8511a5e3 --- /dev/null +++ b/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'corrplot' +version = '0.95' + +homepage = 'https://cran.r-project.org/web/packages/corrplot' +description = """Provides a visual exploratory tool on correlation matrix that supports automatic +variable reordering to help detect hidden patterns among variables..""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['84a31f675041e589201b4d640753302abc10ccc2c0ca0a409b5153861989d776'] + +dependencies = [ + ('R', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['corrplot'], +} + +moduleclass = 'tools' From f5c852ce847e6eb831ead18131574e6b3817294b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 17 Oct 2024 18:50:20 +0200 Subject: [PATCH 239/524] Update corrplot-0.95-foss-2023a.eb - use name template in sources --- easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb b/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb index ebe8511a5e3..45ed4f64a69 100644 --- a/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb +++ b/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = [ 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/rjags/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['84a31f675041e589201b4d640753302abc10ccc2c0ca0a409b5153861989d776'] From 93a776ce8d6d8892fe4ba7557242f67573ccfda8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 17 Oct 2024 19:07:47 +0200 Subject: [PATCH 240/524] fix the vectorization bug of `scipy-1.11.1` --- .../SciPy-bundle-2023.07-gfbf-2023a.eb | 4 + .../SciPy-bundle-2023.11-gfbf-2023b.eb | 4 + .../scipy-1.11.1_vectorization_error.patch | 104 ++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index 9805854b0c3..a70dd43dfa6 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), # required by scipy + ('Cython', '3.0.8'), ] dependencies = [ @@ -73,12 +74,15 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.11.1_vectorization_error.patch', ], 'checksums': [ {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.11.1_vectorization_error.patch': + 'a28a7a11cc7129fe0e8d482e1ced30083bb6ab35642c517e3e2a66839db3111d'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb index ae7ab11bbc4..2efdde8cea3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb @@ -17,6 +17,7 @@ builddependencies = [ ('meson-python', '0.15.0'), ('Ninja', '1.11.1'), ('pkgconf', '2.0.3'), # required by scipy + ('Cython', '3.0.10'), ] dependencies = [ @@ -68,6 +69,7 @@ exts_list = [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', 'scipy-1.11.4_fix-deps-ellip_harm_2.patch', + 'scipy-1.11.1_vectorization_error.patch', ], 'checksums': [ {'scipy-1.11.4.tar.gz': '90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa'}, @@ -76,6 +78,8 @@ exts_list = [ '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, {'scipy-1.11.4_fix-deps-ellip_harm_2.patch': '5c3b4d4dab76cd4c9398c87e6a67b39e3806994ef955fa35781b49f9f99328a8'}, + {'scipy-1.11.1_vectorization_error.patch': + 'a28a7a11cc7129fe0e8d482e1ced30083bb6ab35642c517e3e2a66839db3111d'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch new file mode 100644 index 00000000000..f4929ecc6a0 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch @@ -0,0 +1,104 @@ +Fixes the vectorization bug. see https://github.com/scipy/scipy/issues/16792 +patch source: https://github.com/scipy/scipy/pull/20195 +--- scipy/linalg/_cythonized_array_utils.pyx.orig ++++ scipy/linalg/_cythonized_array_utils.pyx +@@ -158,7 +158,7 @@ + + + @cython.initializedcheck(False) +-def bandwidth_c(np_numeric_t[:, ::1]A): ++def bandwidth_c(const np_numeric_t[:, ::1]A): + cdef int l, u + with nogil: + l, u = band_check_internal_c(A) +@@ -166,7 +166,7 @@ + + + @cython.initializedcheck(False) +-def bandwidth_noncontig(np_numeric_t[:, :]A): ++def bandwidth_noncontig(const np_numeric_t[:, :]A): + cdef int l, u + with nogil: + l, u = band_check_internal_noncontig(A) +@@ -176,7 +176,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline (int, int) band_check_internal_c(np_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline (int, int) band_check_internal_c(const np_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], m = A.shape[1] + cdef Py_ssize_t lower_band = 0, upper_band = 0, r, c + cdef np_numeric_t zero = 0 +@@ -207,7 +207,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline (int, int) band_check_internal_noncontig(np_numeric_t[:, :]A) noexcept nogil: ++cdef inline (int, int) band_check_internal_noncontig(const np_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], m = A.shape[1] + cdef Py_ssize_t lower_band = 0, upper_band = 0, r, c + cdef np_numeric_t zero = 0 +@@ -324,7 +324,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_real_c(np_numeric_t[:, ::1]A): ++def is_sym_her_real_c(const np_numeric_t[:, ::1]A): + cdef bint s + with nogil: + s = is_sym_her_real_c_internal(A) +@@ -332,7 +332,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_real_noncontig(np_numeric_t[:, :]A): ++def is_sym_her_real_noncontig(const np_numeric_t[:, :]A): + cdef bint s + with nogil: + s = is_sym_her_real_noncontig_internal(A) +@@ -342,7 +342,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_real_c_internal(np_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline bint is_sym_her_real_c_internal(const np_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -355,7 +355,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_real_noncontig_internal(np_numeric_t[:, :]A) noexcept nogil: ++cdef inline bint is_sym_her_real_noncontig_internal(const np_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -469,7 +469,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_complex_c(np_complex_numeric_t[:, ::1]A): ++def is_sym_her_complex_c(const np_complex_numeric_t[:, ::1]A): + cdef bint s + with nogil: + s = is_sym_her_complex_c_internal(A) +@@ -485,7 +485,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_complex_c_internal(np_complex_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline bint is_sym_her_complex_c_internal(const np_complex_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -497,7 +497,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_complex_noncontig_internal(np_complex_numeric_t[:, :]A) noexcept nogil: ++cdef inline bint is_sym_her_complex_noncontig_internal(const np_complex_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): + From fc5c77d1b2fbe4a2357f2bfed5d53860c8b040fe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 17:09:41 +0000 Subject: [PATCH 241/524] test suite --- .../easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 209a1027257..098027eecd6 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -29,17 +29,22 @@ dependencies = [ use_pip = True -local_pytest_cmd = 'pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py' - exts_list = [ ('unidist', '0.7.1', { 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], }), + # Cannot test for Ray due to unix socket issue (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], - 'runtest': "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=ray pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py", + 'runtest': ( + "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas " + " --ignore=modin/tests/pandas/test_io.py " + "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" + " MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" + " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From d153d6e46ace73687250fdad86c2d49d654d9f69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 17 Oct 2024 19:09:54 +0200 Subject: [PATCH 242/524] adding easyconfigs: scTIE-20231205-foss-2023a-CUDA-12.1.1.eb, POT-0.9.3-foss-2023a-CUDA-12.1.1.eb, CVXOPT-1.3.2-foss-2023a.eb --- .../c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb | 49 +++++++++++++++++++ .../p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb | 47 ++++++++++++++++++ .../scTIE-20231205-foss-2023a-CUDA-12.1.1.eb | 46 +++++++++++++++++ 3 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb new file mode 100644 index 00000000000..d6793ad49bb --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.3.2' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['CVXOPT-1.3.1_fix-setup-py.patch'] + +checksums = [ + '3461fa42c1b2240ba4da1d985ca73503914157fc4c77417327ed6d7d85acdbe6', # cvxopt-1.3.2.tar.gz + '350904c0427d4652fc73b95b7e0d78a17c917cb94ed6c356dbbbfb07f2173849', # CVXOPT-1.3.1_fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.11.3'), + ('SuiteSparse', '7.1.0'), + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = " ".join([ + 'CVXOPT_BUILD_FFTW=1', + 'CVXOPT_BUILD_GSL=1', + 'CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBBLAS"', + 'CVXOPT_LAPACK_EXTRA_LINK_ARGS="$LIBLAPACK"', + 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT"', + 'CVXOPT_SUITESPARSE_LIB_DIR=$EBROOTSUITESPARSE/lib', + 'CVXOPT_SUITESPARSE_INC_DIR=$EBROOTSUITESPARSE/include', +]) + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && python -m unittest discover -s tests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1eddcba72f5 --- /dev/null +++ b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'POT' +version = '0.9.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/rflamary/POT' +description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems + related to Optimal Transport for signal, image processing and machine learning.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('jax', '0.4.25', versionsuffix), + ('CVXOPT', '1.3.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('autograd', '1.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['49680300f842f3a8722b060ac0d3ed7aca071d1ad4d3d38c9fdadafdcc73c30b'], + }), + ('versioneer', '0.29', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0f1a137bb5d6811e96a79bb0486798aeae9b9c6efc24b389659cebb0ee396cb9'], + }), + ('pymanopt', '2.2.1', { + # Requirements forbid some versions of `scipy` which are known to have a bug but we have fixed it. + # see `scipy-1.11.1_vectorization_error.patch` + 'preinstallopts': """sed -i 's/"scipy>=1.0[^"]*"/"scipy>=1.0"/g' pyproject.toml && """, + 'checksums': ['c784929a436eb06d73371b53ae5db3cdc19c5e60280f8131553bc805cbf7a1da'], + }), + (name, version, { + 'modulename': 'ot', + 'checksums': ['eecf2394390a73472e727ef75f7c801fc47509039f00c40f8fc64fdeea617c86'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..375e693aeba --- /dev/null +++ b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'scTIE' +version = '20231205' +local_commit = '044d91a' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/SydneyBioX/scTIE' +description = """scTIE (single-cell Temporal Integration and inference of multimodal Experiments) + is an autoencoder-based method for integrating multimodal profiling of scRNA-seq and scATAC-seq + data over a time course and inferring cell-type specific GRNs. scTIE projects cells from all time + points into a common embedding space, followed by extracting interpretable information from this + space to predict cell trajectories.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'SydneyBioX' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['bcbf7c846539d0f04e7bbf3cc6ae2fe075a4ba11e3a4388c29def943d39af53e'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('POT', '0.9.3', versionsuffix), +] + +postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -r -s main.py bin/sctie && chmod a+x main.py'] + +fix_python_shebang_for = ['main.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['bin/sctie'], + 'dirs': [], +} + +sanity_check_commands = ['sctie --help'] + +moduleclass = 'bio' From da0530e5da3054612f0378e6cbdfd545b92c489d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 17:37:29 +0000 Subject: [PATCH 243/524] test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 098027eecd6..57ceac35c95 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,10 +39,10 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas " + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas " " --ignore=modin/tests/pandas/test_io.py " "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" - " MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" + " MODIN_ENGINE=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" ), 'source_tmpl': '%(version)s.tar.gz', From e6198a162675109a4532b01707645fdd52f19958 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:09:03 +0000 Subject: [PATCH 244/524] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 57ceac35c95..b08f03c0975 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,11 +39,8 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas " - " --ignore=modin/tests/pandas/test_io.py " - "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" - " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py &&" + " MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 8c1264bc5b5dbc4f21c59b5dc53823d9a8545777 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:14:12 +0000 Subject: [PATCH 245/524] removed unneeded deps --- easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb index 09fd361f0dd..9177b8c01b8 100644 --- a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb @@ -21,15 +21,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('jmespath', '1.0.1', { - 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], - }), - ('botocore', '1.35.36', { - 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], - }), - ('aioitertools', '0.12.0', { - 'checksums': ['c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b'], - }), ('fsspec', version, { 'checksums': ['4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8'], }), From d31ae4f9f1d0d6b3be1eddab4a9120bc43db2510 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:26:47 +0000 Subject: [PATCH 246/524] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index b08f03c0975..5d6a7971f53 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,8 +39,8 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_reshape.py &&" + " MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 88ec16cd3e4fa8f0631d13d17ac684022461d24b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:36:33 +0000 Subject: [PATCH 247/524] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5d6a7971f53..5bc7ac030db 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,8 +39,7 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_reshape.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 3296c1bf546577e954fb69734a4241ff2499981d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:48:45 +0000 Subject: [PATCH 248/524] removed unidist due to non-functionality --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5bc7ac030db..69879efa8ab 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -30,15 +30,12 @@ dependencies = [ use_pip = True exts_list = [ - ('unidist', '0.7.1', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], - 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], - }), + # modin has another backend, "unidist", for MPI, but it seems broken currently. # Cannot test for Ray due to unix socket issue (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( + "MODIN_ENGINE=ray pytest modin/tests/pandas/test_reshape.py &&" "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', From 0b3866d13d01f831366a08938528ca7a126cc405 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:53:18 +0000 Subject: [PATCH 249/524] adding easyconfigs: wrapt-1.16.0-gfbf-2024a.eb --- .../w/wrapt/wrapt-1.16.0-gfbf-2024a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb new file mode 100644 index 00000000000..10f6d8cf5cf --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.16.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), +] + +moduleclass = 'tools' From 54574e3a6c8174df50ae12d4d54c03ddbf10bb5f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:56:59 +0000 Subject: [PATCH 250/524] confirmed ray non-functional tests --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 69879efa8ab..128dd0aae8c 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -31,12 +31,11 @@ use_pip = True exts_list = [ # modin has another backend, "unidist", for MPI, but it seems broken currently. - # Cannot test for Ray due to unix socket issue + # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=ray pytest modin/tests/pandas/test_reshape.py &&" - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 9eef90ae526237506465911e6a099c83ecb52663 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 21:14:01 +0000 Subject: [PATCH 251/524] removed mpi4py dep --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 128dd0aae8c..388c781b8b5 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -24,7 +24,6 @@ dependencies = [ ('OpenMPI', '5.0.3'), ('Ray-project', '2.37.0'), ('Arrow', '17.0.0'), - ('mpi4py', '4.0.1') ] use_pip = True From 0f41afd7220a6b3c04cfe8de50f0b5e2b5b9d8f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Oct 2024 06:20:39 +0200 Subject: [PATCH 252/524] add `scipy` bug description --- .../s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb | 2 +- .../s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb | 2 +- .../s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index a70dd43dfa6..424296cf1fe 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -82,7 +82,7 @@ exts_list = [ {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, {'scipy-1.11.1_vectorization_error.patch': - 'a28a7a11cc7129fe0e8d482e1ced30083bb6ab35642c517e3e2a66839db3111d'}, + 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb index 2efdde8cea3..38fb986242d 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb @@ -79,7 +79,7 @@ exts_list = [ {'scipy-1.11.4_fix-deps-ellip_harm_2.patch': '5c3b4d4dab76cd4c9398c87e6a67b39e3806994ef955fa35781b49f9f99328a8'}, {'scipy-1.11.1_vectorization_error.patch': - 'a28a7a11cc7129fe0e8d482e1ced30083bb6ab35642c517e3e2a66839db3111d'}, + 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch index f4929ecc6a0..6cf77dee6f5 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch @@ -1,4 +1,5 @@ -Fixes the vectorization bug. see https://github.com/scipy/scipy/issues/16792 +Fixes the vectorization bug. `ValueError: buffer source array is read-only` +see https://github.com/scipy/scipy/issues/16792 patch source: https://github.com/scipy/scipy/pull/20195 --- scipy/linalg/_cythonized_array_utils.pyx.orig +++ scipy/linalg/_cythonized_array_utils.pyx From 1a2c3137d3b8aed2d8750c368562308749d7665b Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 09:57:50 +0200 Subject: [PATCH 253/524] change GMAP-GSNAP version --- easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb index 1ee3e15c13f..8d42086755c 100644 --- a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb @@ -18,7 +18,7 @@ checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] dependencies = [ ('SQLite', '3.42.0'), - ('GMAP-GSNAP', '2024-09-18'), + ('GMAP-GSNAP', '2023-04-20'), ('pblat', '2.5.1'), ('minimap2', '2.26'), ('FASTA', '36.3.8i'), From 0d3fc4d53b37eed81d289a4e26109b0aadc1a48c Mon Sep 17 00:00:00 2001 From: "Bindeus,Alexander" Date: Fri, 18 Oct 2024 10:54:32 +0200 Subject: [PATCH 254/524] adding easyconfigs: Nextflow-24.04.4.eb --- .../n/Nextflow/Nextflow-24.04.4.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb new file mode 100644 index 00000000000..c718972b663 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '24.04.4' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-all'] +checksums = ['9077cfb151d4bc8682f09a65a77f45346bf34dac5931e371dba0d51bf13a5076'] + +dependencies = [('Java', '11')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + +moduleclass = 'tools' From ffcf2425760998e2dfab16e2a4789d1dfd5b0301 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 18 Oct 2024 11:30:23 +0200 Subject: [PATCH 255/524] move corrplot to exts --- ...sDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb | 28 +++++++++++++++++-- .../c/corrplot/corrplot-0.95-foss-2023a.eb | 28 ------------------- 2 files changed, 25 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb index d61b8779821..76a00927a51 100644 --- a/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb @@ -19,16 +19,38 @@ checksums = ['4ba5967fa754ec78b9dd6b6dc9d2ee5de87dbb4d7906d47e57e73aec87897725'] dependencies = [ ('Python', '2.7.18'), + ('R', '4.3.2'), ('numpy', '1.16.6', versionsuffix), - ('corrplot', '0.95'), ] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('corrplot', '0.95', { + 'checksums': ['84a31f675041e589201b4d640753302abc10ccc2c0ca0a409b5153861989d776'], + }), +] + files_to_copy = [(['learnDiverseModules'], 'bin')] +modextrapaths = {'R_LIBS_SITE': ''} + sanity_check_paths = { 'files': ['bin/learnDiverseModules'], - 'dirs': [], + 'dirs': ['corrplot'], } -sanity_check_commands = ['learnDiverseModules -h'] +sanity_check_commands = [ + 'learnDiverseModules -h', + 'Rscript -e "library(corrplot)"', +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb b/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb deleted file mode 100644 index 45ed4f64a69..00000000000 --- a/easybuild/easyconfigs/c/corrplot/corrplot-0.95-foss-2023a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'RPackage' - -name = 'corrplot' -version = '0.95' - -homepage = 'https://cran.r-project.org/web/packages/corrplot' -description = """Provides a visual exploratory tool on correlation matrix that supports automatic -variable reordering to help detect hidden patterns among variables..""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['84a31f675041e589201b4d640753302abc10ccc2c0ca0a409b5153861989d776'] - -dependencies = [ - ('R', '4.3.2'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['corrplot'], -} - -moduleclass = 'tools' From 4fe1739c6e3f45e1061fd18421b3cda6315249e3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 18 Oct 2024 12:03:02 +0200 Subject: [PATCH 256/524] use magic string in patch for tenacity --- .../p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb | 3 ++- .../easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch | 5 +++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb index 86f3008c630..97bb6e12c8d 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb @@ -20,9 +20,10 @@ use_pip = True exts_list = [ ('tenacity', '9.0.0', { 'patches': ['tenacity-9.0.0_fix_version.patch'], + 'preinstallopts': "sed -i 's/EB_TENACITY_VERSION/%(version)s/' setup.cfg && ", 'checksums': [ {'tenacity-9.0.0.tar.gz': '807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b'}, - {'tenacity-9.0.0_fix_version.patch': '7adb47c0a86b6dcfa075a98caa1532f9212f7c6b5f219d205e88b7aa97aa46a0'}, + {'tenacity-9.0.0_fix_version.patch': '71a533470f03aab802439bda078494ab98804439afdb16f8287337bd3e0c8a82'}, ], }), ('packaging', '24.1', { diff --git a/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch index 840d0b75f8c..9bd6e65af16 100644 --- a/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch +++ b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch @@ -1,6 +1,7 @@ # What: Putting a manually typed version in setup.cfg, as it wouldnt resolve automatically. # Author: Denis Kristak (Inuits)diff -ruN tenacity-8.2.3_orig/setup.cfg tenacity-8.2.3/setup.cfg -# Updated for v9.0.0 by maxim-masterov (SURF) +# Updated for v9.0.0 by maxim-masterov (SURF) +# Updated with magic string to avoid having to update the patch for every version by Samuel Moors (Vrije Universiteit Brussel) diff -Nru tenacity-9.0.0.orig/setup.cfg tenacity-9.0.0/setup.cfg --- tenacity-9.0.0.orig/setup.cfg 2024-10-10 16:50:28.669538307 +0200 +++ tenacity-9.0.0/setup.cfg 2024-10-10 16:50:54.881500726 +0200 @@ -8,7 +9,7 @@ diff -Nru tenacity-9.0.0.orig/setup.cfg tenacity-9.0.0/setup.cfg [metadata] name = tenacity license = Apache 2.0 -+version = 9.0.0 ++version = 'EB_TENACITY_VERSION' url = https://github.com/jd/tenacity summary = Retry code until it succeeds long_description = Tenacity is a general-purpose retrying library to simplify the task of adding retry behavior to just about anything. From 51f07a06857955ff44197f8a67cfa05af06b6370 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:07:03 +0200 Subject: [PATCH 257/524] adding easyconfigs: LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb, LightGBM-4.5.0-foss-2023a.eb, LightGBM-4.5.0-foss-2023a.eb --- .../LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb | 56 +++++++++++++++++++ .../l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 32 +++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..79b61c8d87b --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional +] + +use_pip = True + +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_CUDA=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb new file mode 100644 index 00000000000..0cf659abfae --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['0000000000000000000000000000000000000000000000000000000000000000'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 819ed9cf8eb306e0abf92020b81ffd96d9aa4331 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:14:58 +0200 Subject: [PATCH 258/524] fix LightGBM-4.5.0-foss-2023a.eb --- .../l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 26 +++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb index 0cf659abfae..fdbf6f54f1d 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -11,19 +11,41 @@ classification and many other machine learning tasks.""" toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ - ('CMake', '3.26.3'), + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), ] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional ] use_pip = True +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + exts_list = [ ('lightgbm', version, { - 'checksums': ['0000000000000000000000000000000000000000000000000000000000000000'], + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_MPI=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, }), ] From 02e8e5a5273a118571ac0c65ec5da5faea38e4cb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:15:35 +0200 Subject: [PATCH 259/524] adding easyconfig: scikit-build-core-0.9.3-GCCcore-12.3.0.eb --- .../scikit-build-core-0.9.3-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a17cdb279fe --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.9.3' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CMake', '3.26.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('scikit_build_core', version, { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), +] + +moduleclass = 'lib' From 0918cffb46ca1737e35fd0aef08c41a072aef306 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Fri, 18 Oct 2024 12:20:22 +0000 Subject: [PATCH 260/524] added unidist problem info --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 388c781b8b5..5ed0e424dfd 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -30,6 +30,7 @@ use_pip = True exts_list = [ # modin has another backend, "unidist", for MPI, but it seems broken currently. + # The unidist backend will just fire up all cores as if initializing but not actually advance. # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], From 4a062587284e0ce5c73b9689c731cdb33094ddb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Oct 2024 14:20:50 +0200 Subject: [PATCH 261/524] adding easyconfigs: BRAKER-3.0.8-foss-2023a.eb, spaln-3.0.6a-GCC-12.3.0.eb --- .../b/BRAKER/BRAKER-3.0.8-foss-2023a.eb | 55 +++++++++++++++++++ .../s/spaln/spaln-3.0.6a-GCC-12.3.0.eb | 49 +++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb new file mode 100644 index 00000000000..7a87a70ddb1 --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb @@ -0,0 +1,55 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'Tarball' + +name = 'BRAKER' +version = '3.0.8' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2623290c3007a3e42719a0bb2713bec7226db222bfef742895a9d5d0b4ee526'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('AUGUSTUS', '3.5.0'), + ('GeneMark-ET', '4.72'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.18'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), + ('spaln', '3.0.6b'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.14.1'), + ('Biopython', '1.83'), + ('DIAMOND', '2.1.8'), + ('CDBtools', '0.99'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': [ + 'scripts/braker.pl', + 'scripts/compare_intervals_exact.pl', + 'scripts/compute_accuracies.sh', + 'scripts/compute_accuracies.sh', + 'scripts/filterGenemark.pl', + 'scripts/findGenesInIntrons.pl', + 'scripts/gatech_pmp2hints.pl', + 'scripts/sortGeneMark.py', + ], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb new file mode 100644 index 00000000000..0cdb496871d --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '3.0.6a' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver.%(version)s.tar.gz'] +checksums = ['63c46589374e7c2b9a767ef3170504637cb2a57a05d0090a1a8bc6656cd3f254'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), +] + +start_dir = 'src' + +# not a standard `configure` - does not accept standard `--prefix` option +# see https://github.com/ogotoh/spaln/issues/74 +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb" + +installopts = 'DESTDIR=%(installdir)s/' + +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' From e604d3619a287099c3105c52de9a6b9eb67f9f6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Oct 2024 14:28:05 +0200 Subject: [PATCH 262/524] correct version of `spaln` --- .../s/spaln/spaln-3.0.6b-GCC-12.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb new file mode 100644 index 00000000000..18fe5408f73 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '3.0.6b' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver.%(version)s.tar.gz'] +checksums = ['8e496ef6d02696543f4a5e31922f464555eff9b8405da366587ba7bea27b4e76'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), +] + +start_dir = 'src' + +# not a standard `configure` - does not accept standard `--prefix` option +# see https://github.com/ogotoh/spaln/issues/74 +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb" + +installopts = 'DESTDIR=%(installdir)s/' + +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' From fdb168155c6facf9c2c5c26c92df5079be48e4fe Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 18 Oct 2024 14:33:22 +0200 Subject: [PATCH 263/524] fix likwid-5.3.0-GCC-13.3.0.eb --- .../l/likwid/likwid-5.3.0-GCC-13.3.0.eb | 33 +++++++++---------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb index a23dea7326c..b9d22fc36dc 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb @@ -4,6 +4,7 @@ name = 'likwid' version = '5.3.0' homepage = 'https://github.com/RRZE-HPC/likwid' + description = """ Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high @@ -15,6 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] + checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] builddependencies = [ @@ -24,32 +26,29 @@ dependencies = [ ('hwloc', '2.10.0'), ] +skipsteps = ['configure'] + # include_GCC.mk is using ifort by default. # Changing it to gfortran, to be consistent with GCC toolchain -prebuildopts = "sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && " -prebuildopts += "sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' make/include_GCC.mk " -prebuildopts += "&& " +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' -buildopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' -installopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' -installopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' -installopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' -installopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' -installopts += 'INSTALL_CHOWN="" ' - maxparallel = 1 -skipsteps = ['configure'] +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { - 'files': ['bin/%(name)s-memsweeper', 'bin/%(name)s-mpirun', 'bin/%(name)s-perfctr', 'bin/%(name)s-perfscope', - 'bin/%(name)s-pin', 'bin/%(name)s-powermeter', 'bin/%(name)s-topology', 'lib/liblikwidpin.so', - 'lib/liblikwid.so', 'include/%(name)s.mod'], - 'dirs': ['man/man1'], + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] } moduleclass = 'tools' From 8cf898edf91d0c3e8b5b109b061f6dce1d684522 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 18 Oct 2024 13:15:15 +0200 Subject: [PATCH 264/524] fix CI check for extension patches using `alt_location` While `alt_location` can be used for patches in the main EasyConfig part and in extensions the verification code handled them differently and missed to take the `alt_location` into account for extension patches. Factor our the checking code to a function that can be used for both cases. This also removes a redundant condition in one of the code instances before verifying the checksums. --- test/easyconfigs/easyconfigs.py | 83 +++++++++++++++++++-------------- 1 file changed, 48 insertions(+), 35 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0626f94e5f3..eca5c4e2add 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1365,6 +1365,51 @@ def test_pr_patch_descr(self): self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) +def verify_patch(specdir, patch_spec, checksum_idx, patch_checksums, extension_name=None): + """Verify existance and checksum of the given patch. + + specdir - Directory of the easyconfig + patch_spec - Patch entry + checksum_idx - Expected index in the checksum list + patch_checksums - List of checksums for patches + extension_name - Name of the extensions this patch is for if any + + Return a (possibly empty) list of failure messages + """ + patch_dir = specdir + if isinstance(patch_spec, str): + patch_name = patch_spec + elif isinstance(patch_spec, (tuple, list)): + patch_name = patch_spec[0] + elif isinstance(patch_spec, dict): + patch_name = patch_spec['name'] + alt_location = patch_spec.get('alt_location') + if alt_location: + basedir = os.path.dirname(os.path.dirname(specdir)) + patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) + else: + # Should have already been verified + raise RuntimeError('Patch spec is not a string, tuple, list or dict: %s\nType: %s' % (patch_spec, + type(patch_spec))) + + patch_path = os.path.join(patch_dir, patch_name) + patch_descr = "patch file " + patch_name + if extension_name: + patch_descr += "of extension " + extension_name + + # only check actual patch files, not other files being copied via the patch functionality + if patch_path.endswith('.patch'): + if not os.path.isfile(patch_path): + return [patch_descr + "is missing"] + + if checksum_idx < len(patch_checksums): + checksum = patch_checksums[checksum_idx] + if not verify_checksum(patch_path, checksum): + return ["Invalid checksum for %s: %s" % (patch_descr, checksum)] + + return [] # No error + + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" @@ -1516,27 +1561,9 @@ def template_easyconfig_test(self, spec): # make sure all patch files are available specdir = os.path.dirname(spec) - basedir = os.path.dirname(os.path.dirname(specdir)) + for idx, patch in enumerate(patches): - patch_dir = specdir - if isinstance(patch, str): - patch_name = patch - elif isinstance(patch, (tuple, list)): - patch_name = patch[0] - elif isinstance(patch, dict): - patch_name = patch['name'] - if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(patch['alt_location']), patch['alt_location']) - - # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(patch_dir, patch_name) - if patch_name.endswith('.patch') and not os.path.isfile(patch_full): - failing_checks.append("Patch file %s is missing" % patch_full) - # verify checksum for each patch file - elif idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): - checksum = patch_checksums[idx] - if not verify_checksum(patch_full, checksum): - failing_checks.append("Invalid checksum for patch file %s: %s" % (patch_name, checksum)) + failing_checks.extend(verify_patch(specdir, patch, idx, patch_checksums)) # make sure 'source' step is not being skipped, # since that implies not verifying the checksum @@ -1566,21 +1593,7 @@ def template_easyconfig_test(self, spec): patch_checksums = checksums[src_cnt:] for idx, ext_patch in enumerate(ext.get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch['name']) - if ext_patch_full.endswith('.patch') and not os.path.isfile(ext_patch_full): - failing_checks.append("Patch file %s for extension %s is missing." % (ext_patch['name'], ext_name)) - continue - - # verify checksum for each patch file - if idx < len(patch_checksums) and os.path.exists(ext_patch_full): - checksum = patch_checksums[idx] - if not verify_checksum(ext_patch_full, checksum): - failing_checks.append("Invalid checksum for patch %s for extension %s: %s." - % (ext_patch['name'], ext_name, checksum)) + failing_checks.extend(verify_patch(specdir, ext_patch, idx, patch_checksums, extension_name=ext_name)) # check whether all extra_options defined for used easyblock are defined extra_opts = app.extra_options() From 312b92d01f37b62ab752b8d25be9f040af0fdaf6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Oct 2024 15:08:31 +0200 Subject: [PATCH 265/524] fix the zero division bug of `networkx-3.1` --- .../n/networkx/networkx-3.1-gfbf-2023a.eb | 6 ++- .../networkx/networkx-3.1_zero_division.patch | 42 +++++++++++++++++++ 2 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb index 2cef5135036..03fe29675fd 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb @@ -10,7 +10,11 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'gfbf', 'version': '2023a'} sources = [SOURCE_TAR_GZ] -checksums = ['de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61'] +patches = ['networkx-3.1_zero_division.patch'] +checksums = [ + {'networkx-3.1.tar.gz': 'de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61'}, + {'networkx-3.1_zero_division.patch': 'fb225e9942f18c87c67b49093b86e9f949e043fdf2f3c1ed467b6d3ad857aa35'}, +] dependencies = [ ('Python', '3.11.3'), diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch b/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch new file mode 100644 index 00000000000..3110ca55530 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch @@ -0,0 +1,42 @@ +Fixes the zero division bug `ZeroDivisionError: division by zero` +patch source: https://github.com/networkx/networkx/pull/6791 + +From 6e47bef10ba7c17514b0cbd2ec27c1f58ca21200 Mon Sep 17 00:00:00 2001 +From: juanis2112 +Date: Sat, 15 Jul 2023 14:22:02 -0500 +Subject: [PATCH] Fix empty graph zero division error for louvain + +--- + networkx/algorithms/community/louvain.py | 3 +++ + networkx/algorithms/community/tests/test_louvain.py | 7 +++++++ + 2 files changed, 10 insertions(+) + +diff --git a/networkx/algorithms/community/louvain.py b/networkx/algorithms/community/louvain.py +index ca71c0c30cb..94a8f7c98b9 100644 +--- a/networkx/algorithms/community/louvain.py ++++ b/networkx/algorithms/community/louvain.py +@@ -163,6 +163,9 @@ def louvain_partitions( + """ + + partition = [{u} for u in G.nodes()] ++ if nx.is_empty(G): ++ yield partition ++ return + mod = modularity(G, partition, resolution=resolution, weight=weight) + is_directed = G.is_directed() + if G.is_multigraph(): +diff --git a/networkx/algorithms/community/tests/test_louvain.py b/networkx/algorithms/community/tests/test_louvain.py +index ed5c2a38db6..e4942dfeb58 100644 +--- a/networkx/algorithms/community/tests/test_louvain.py ++++ b/networkx/algorithms/community/tests/test_louvain.py +@@ -185,3 +185,10 @@ def test_threshold(): + mod2 = nx.community.modularity(G, partition2) + + assert mod1 < mod2 ++ ++ ++def test_empty_graph(): ++ G = nx.Graph() ++ G.add_nodes_from(range(5)) ++ expected = [{0}, {1}, {2}, {3}, {4}] ++ assert nx.community.louvain_communities(G) == expected From 37062deeb6ecd5ff4db81a7142ac559694145afc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Oct 2024 15:11:21 +0200 Subject: [PATCH 266/524] adding easyconfigs: CIRCE-0.3.4-foss-2023a.eb --- .../c/CIRCE/CIRCE-0.3.4-foss-2023a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb b/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb new file mode 100644 index 00000000000..6a41b512096 --- /dev/null +++ b/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'CIRCE' +version = '0.3.4' + +homepage = 'https://github.com/cantinilab/Circe' +description = """This repo contains a python package for inferring co-accessibility networks + from single-cell ATAC-seq data, using skggm for the graphical lasso and scanpy for data processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), +] + +use_pip = True +sanity_pip_check = True + +# Some requirements are too strict. +local_preinstallopts = """sed -i 's/pandas = "[^"]*"/pandas = "*"/g' pyproject.toml && """ +local_preinstallopts += """sed -i "s/'pandas>=[^']*'/'pandas'/g" setup.py && """ + +# build the C components linking `flexiblas` instead of `lapack` and `blas` +local_preinstallopts += """sed -i "s/lapack/flexiblas/g;s/, 'blas'//g" setup.py && """ +local_preinstallopts += """sed -i "s/lapack/flexiblas/g;/blas/d" pyquic_ext/pyquic.cpp && """ + +exts_list = [ + ('joblib', '1.4.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6'], + }), + ('rich', '13.9.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1'], + }), + ('circe_py', version, { + 'preinstallopts': local_preinstallopts, + 'modulename': 'circe', + 'checksums': ['279004948dff84816361e857ee3fb383cdb17587f376c6f10f82a66810cba16c'], + }), +] + +# NOTE This has been tested manually using the following script: +# https://github.com/cantinilab/Circe/blob/a70e031f9de4760739eb3c7571277678d5e80c8a/Examples/Minimal_example.ipynb +# with a small modification: +# https://github.com/cantinilab/Circe/issues/5#issuecomment-2419821380 + +moduleclass = 'bio' From 9142fd21107c78a49fc7aef64b6987366e41b486 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 15:57:23 +0200 Subject: [PATCH 267/524] Add wrapper for trimmomatic --- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb | 6 +++++- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb index b5a28e53771..d9d815718c9 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb @@ -22,7 +22,11 @@ checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] dependencies = [('Java', '11')] -modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" +postinstallcmds = [ + "mkdir %(installdir)s/bin", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + "chmod a+rx %(installdir)s/bin/trimmomatic", +] sanity_check_paths = { 'files': ["trimmomatic-%(version)s.jar"], diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb index 5f9d39b5c69..c0706322ea6 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb @@ -22,7 +22,11 @@ checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] dependencies = [('Java', '17')] -modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" +postinstallcmds = [ + "mkdir %(installdir)s/bin", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + "chmod a+rx %(installdir)s/bin/trimmomatic", +] sanity_check_paths = { 'files': ["trimmomatic-%(version)s.jar"], From 2c9b28bc7e028d1225c709f81f6322a3e77c9c21 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 16:08:18 +0200 Subject: [PATCH 268/524] adding easyconfigs: CodingQuarry-2.0-foss-2023a.eb, DBD-mysql-4.050-GCC-12.3.0.eb, GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb, GlimmerHMM-3.0.4c-GCC-12.3.0.eb, Infernal-1.1.5-foss-2023a.eb, Jellyfish-2.3.1-GCC-12.3.0.eb, Proteinortho-6.3.2-gompi-2023a.eb, RSEM-1.3.3-foss-2023a-Java-11.eb, SNAP-HMM-20221022-GCC-12.3.0.eb, StringTie-2.2.3-GCC-12.3.0.eb, Trinity-2.15.1-foss-2023a.eb, eggnog-mapper-2.1.12-foss-2023a.eb, funannotate-1.8.17-foss-2023a.eb, tRNAscan-SE-2.0.12-foss-2023a.eb, tantan-50-GCC-12.3.0.eb --- .../CodingQuarry-2.0-foss-2023a.eb | 51 ++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb | 30 ++++++ .../eggnog-mapper-2.1.12-foss-2023a.eb | 56 +++++++++++ .../funannotate-1.8.17-foss-2023a.eb | 96 +++++++++++++++++++ .../GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb | 54 +++++++++++ .../GlimmerHMM-3.0.4c-GCC-12.3.0.eb | 57 +++++++++++ .../i/Infernal/Infernal-1.1.5-foss-2023a.eb | 39 ++++++++ .../j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb | 40 ++++++++ .../Proteinortho-6.3.2-gompi-2023a.eb | 34 +++++++ .../r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb | 55 +++++++++++ .../SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb | 45 +++++++++ .../s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb | 49 ++++++++++ .../t/Trinity/Trinity-2.15.1-foss-2023a.eb | 64 +++++++++++++ .../tRNAscan-SE-2.0.12-foss-2023a.eb | 42 ++++++++ .../t/tantan/tantan-50-GCC-12.3.0.eb | 26 +++++ 15 files changed, 738 insertions(+) create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb create mode 100644 easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb new file mode 100644 index 00000000000..4757b9125f2 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'CodingQuarry' +version = '2.0' + +homepage = 'https://sourceforge.net/p/codingquarry' +description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['CodingQuarry_v%(version)s.tar.gz'] +patches = ['CodingQuarry-2.0_python3.patch'] +checksums = [ + {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, + {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), + 'QuarryFiles', + 'TESTING', +] + +fix_python_shebang_for = [ + 'bin/CufflinksGTF_to_CodingQuarryGFF3.py', + 'QuarryFiles/scripts/*.py', +] + +sanity_check_paths = { + 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'], +} + +sanity_check_commands = [ + "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'", + "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING", + "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3", +] + +modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb new file mode 100644 index 00000000000..eec33081a4c --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('MariaDB', '11.6.0'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb new file mode 100644 index 00000000000..4937c8bba74 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.12' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b3c53fb0e606a5cfec75cbc84f7c215f57f43ce00d8e50f449513acdad76da73'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('HMMER', '3.4'), + ('DIAMOND', '2.1.8'), + ('prodigal', '2.6.3'), + ('wget', '1.24.5'), + ('MMseqs2', '14-7e284'), + ('XlsxWriter', '3.1.3'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb new file mode 100644 index 00000000000..af2d819eeb5 --- /dev/null +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'funannotate' +version = '1.8.17' + +homepage = 'https://funannotate.readthedocs.io' +description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work + with higher eukaryotes)""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# see also https://github.com/nextgenusfs/funannotate/blob/master/docs/dependencies.rst +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('GOATOOLS', '1.4.5'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('DBD-mysql', '4.050'), + ('CodingQuarry', '2.0'), + ('Trinity', '2.15.1'), + ('AUGUSTUS', '3.5.0'), + ('BamTools', '2.5.2'), + ('BEDTools', '2.31.0'), + ('BLAST+', '2.14.1'), # provides makeblastdb, tblastn + ('BLAT', '3.7'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('ETE', '3.1.3'), + ('Exonerate', '2.4.0'), + ('FASTA', '36.3.8i'), + ('GlimmerHMM', '3.0.4c'), + ('GMAP-GSNAP', '2023-04-20'), # provides gmap + ('GeneMark-ET', '4.72'), # provides gmes_petap.pl + ('HISAT2', '2.2.1'), + ('HMMER', '3.4'), # provides hmmscan, hmmsearch + ('kallisto', '0.51.1'), + ('MAFFT', '7.520', '-with-extensions'), + ('minimap2', '2.26'), + ('pigz', '2.8'), + ('Proteinortho', '6.3.2'), + ('Kent_tools', '468'), # provides pslCDnaFilter + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('SignalP', '6.0h', '-fast'), + ('SNAP-HMM', '20221022'), + ('StringTie', '2.2.3'), + ('tRNAscan-SE', '2.0.12'), + ('tantan', '50'), + ('trimAl', '1.4.1'), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), + ('BioPerl', '1.7.8'), + ('EVidenceModeler', '2.1.0'), +] + +#missin installations tRNAscan-SE/2.0.12-foss-2023a, tantan/40-foss-2023a + +use_pip = True + +exts_list = [ + ('distro', '1.9.0', { + 'checksums': ['2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['bdadfd7a5636383c1c40c26dab37c5908a77e8c4064adced84f1ba9e86187a04'], + 'preinstallopts': ( + """sed -i 's|REQUIRES_PYTHON = ">=3.6.0, <3.10"|REQUIRES_PYTHON = ">=3.6.0"|' setup.py && """ + """sed -i 's|"biopython<1.80",|"biopython",|' setup.py && """ + ) + }), +] + +sanity_check_paths = { + 'files': ['bin/funannotate'], + 'dirs': [], +} + +modextrapaths = { + 'GENEMARK_PATH': '$EBROOTGENEMARKMINET', +} + +sanity_check_commands = [ + "funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'", + "funannotate check --show-versions", +] + + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..d21f30ba953 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb new file mode 100644 index 00000000000..ad435033f81 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +dependencies = [ + ('Perl', '5.36.1'), +] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + (['train/*.pm'], 'lib/perl%(perlmajver)s'), + 'trained_dir', 'README', 'train/readme.train', +] + +fix_perl_shebang_for = ['bin/trainGlimmerHMM'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [ + "%(namelower)s -h", + r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'", +] + +modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb new file mode 100644 index 00000000000..7a89f4503eb --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.5" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..b1a629f7f1e --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.1' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb new file mode 100644 index 00000000000..4cd050e7d31 --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Proteinortho' +version = '6.3.2' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/'] +sources = ['proteinortho-v%(version)s.tar.gz'] +checksums = ['3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), +] + +skipsteps = ['configure'] + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "PREFIX=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'], + 'dirs': [], +} + +sanity_check_commands = ["proteinortho --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb new file mode 100644 index 00000000000..dbebc0f591d --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://deweylab.github.io/RSEM/' +description = "RNA-Seq by Expectation-Maximization" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc', # v1.3.3.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('HISAT2', '2.2.1', '-Java-%(javaver)s'), + ('STAR', '2.7.11b'), + ('Bowtie2', '2.5.1'), + ('Bowtie', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb new file mode 100644 index 00000000000..06b3173938e --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20221022' +_commit = '4ad1e95' + +homepage = 'https://korflab.github.io/' +description = """ +SNAP is a general purpose gene finding program suitable for both eukaryotic and +prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid +Parser. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-20190603_makefile_correction.patch'] +checksums = [ + {'20221022.tar.gz': 'a85726b7d4199da1b213b613057600012a392ef1aa20198f1d571fac55bf643f'}, + {'SNAP-HMM-20190603_makefile_correction.patch': 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655'}, +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +files_to_copy = [ + (['hmm-assembler.pl', 'zff2gff3.pl', 'fathom', 'forge', 'snap', 'Zoe/zoe-loop'], 'bin'), + 'DNA', + 'HMM', + 'Zoe', +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/forge', 'bin/zoe-loop'], + 'dirs': ['Zoe'], +} + +sanity_check_commands = [ + 'snap 2>&1 | grep "^usage:"', + 'zoe-loop | grep "^usage:"', +] + +modextrapaths = {'ZOE': 'Zoe'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..b8bf61dd6cf --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.2.3' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f372640b70a8fde763712d2f0565aff71f5facdc2300c8af829fea94a05ff208'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libdeflate', '1.18'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('HTSlib', '1.18'), + ('Python', '3.11.3'), +] + +local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +buildopts = 'release ' + local_libs + +# the test script downloads some test data from the internet +runtest = 'test' +testopts = local_libs + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py3'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help', 'prepDE.py3 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb new file mode 100644 index 00000000000..6b10fd59155 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.5.1'), + ('GMAP-GSNAP', '2023-04-20'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.18'), + ('Jellyfish', '2.3.1'), + ('kallisto', '0.51.1'), + ('ncurses', '6.4'), + ('RSEM', '1.3.3'), + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11b'), + ('zlib', '1.2.13'), +] + +withsampledata = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb new file mode 100644 index 00000000000..a9c9fa5f5c4 --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'http://trna.ucsc.edu/tRNAscan-SE/' +description = """tRNAscan-SE is the most widely employed tool for identifying + and annotating tRNA genes in genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://trna.ucsc.edu/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] + +builddependencies = [ + # tRNAscan-SE's configure script really wants Autoconf 2.69 + ('Autoconf', '2.71', '', SYSTEM), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Infernal', '1.1.5'), +] + +parallel = 1 + +# tRNAscan-SE.conf sets the Infernal bin directory to be ours. +postinstallcmds = [ + "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", +] + +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/tRNAscan-SE', 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm'], + 'dirs': ['include'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb new file mode 100644 index 00000000000..c4a4ce67c25 --- /dev/null +++ b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tantan' +version = '50' + +homepage = 'https://gitlab.com/mcfrith/tantan' +description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/'] +sources = ['tantan-%(version)s.tar.gz'] +checksums = ['a239e9fb3c059ed9eb4c25a29b3c44a2ef1c1b492a9780874f429de7ae8b5407'] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/tantan'], + 'dirs': [], +} + +sanity_check_commands = ["tantan --help"] + +moduleclass = 'bio' From 7b51098e2f4a00b156742bf72786fc10623e4c5a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 16:52:05 +0200 Subject: [PATCH 269/524] add sanity check command and path + make CI happy --- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb | 7 +++++-- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb index d9d815718c9..4108cd9de19 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb @@ -24,13 +24,16 @@ dependencies = [('Java', '11')] postinstallcmds = [ "mkdir %(installdir)s/bin", - """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' """ + """> %(installdir)s/bin/trimmomatic""", "chmod a+rx %(installdir)s/bin/trimmomatic", ] sanity_check_paths = { - 'files': ["trimmomatic-%(version)s.jar"], + 'files': ["trimmomatic-%(version)s.jar", 'bin/trimmomatic'], 'dirs': [""], } +sanity_check_commands = ['trimmomatic -version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb index c0706322ea6..bd49df5d0a8 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb @@ -24,13 +24,16 @@ dependencies = [('Java', '17')] postinstallcmds = [ "mkdir %(installdir)s/bin", - """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' """ + """> %(installdir)s/bin/trimmomatic""", "chmod a+rx %(installdir)s/bin/trimmomatic", ] sanity_check_paths = { - 'files': ["trimmomatic-%(version)s.jar"], + 'files': ["trimmomatic-%(version)s.jar", 'bin/trimmomatic'], 'dirs': [""], } +sanity_check_commands = ['trimmomatic -version'] + moduleclass = 'bio' From fdaf939bb7c537b8361483f6e47cf64c8934ea5c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 21:14:54 +0200 Subject: [PATCH 270/524] fix style --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index af2d819eeb5..22a735ac9af 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -56,8 +56,6 @@ dependencies = [ ('EVidenceModeler', '2.1.0'), ] -#missin installations tRNAscan-SE/2.0.12-foss-2023a, tantan/40-foss-2023a - use_pip = True exts_list = [ From 3f541a45eed06c4e82c7c5ef2f4efd5e31089f54 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 22:00:46 +0200 Subject: [PATCH 271/524] add missing checksums --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb | 1 + easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb index d21f30ba953..c5247c1cf5a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb @@ -33,6 +33,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['gatk-%(version)s.zip'] +checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ ('Java', '11', '', SYSTEM), diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb index b1a629f7f1e..82821a0cc38 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] - +checksums = ['ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd'] parallel = 1 From 15ce961779249b3a64a0d95b40482806c977dfeb Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 18 Oct 2024 23:21:53 +0200 Subject: [PATCH 272/524] Remove wrong references to Java --- ...EM-1.3.3-foss-2023a-Java-11.eb => RSEM-1.3.3-foss-2023a.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/r/RSEM/{RSEM-1.3.3-foss-2023a-Java-11.eb => RSEM-1.3.3-foss-2023a.eb} (94%) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb similarity index 94% rename from easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb rename to easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb index dbebc0f591d..c3170802211 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb @@ -12,7 +12,6 @@ easyblock = 'ConfigureMake' name = 'RSEM' version = '1.3.3' -versionsuffix = '-Java-%(javaver)s' homepage = 'https://deweylab.github.io/RSEM/' description = "RNA-Seq by Expectation-Maximization" @@ -40,7 +39,7 @@ dependencies = [ ('Perl-bundle-CPAN', '5.36.1'), ('R', '4.3.2'), ('R-bundle-CRAN', '2023.12'), - ('HISAT2', '2.2.1', '-Java-%(javaver)s'), + ('HISAT2', '2.2.1'), ('STAR', '2.7.11b'), ('Bowtie2', '2.5.1'), ('Bowtie', '1.3.1'), From 6e9519d25f47bae326abf55415426376987d7aa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Oct 2024 10:04:03 +0200 Subject: [PATCH 273/524] add missing description to patch file for EVidenceModeler --- .../EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch | 2 ++ .../e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch index eae7fcae4ba..3920012f0c7 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch @@ -1,3 +1,5 @@ +take into account $CFLAGS and $CXXFLAGS set in build environment when building ParaFly +author: Lara Peeters (HPC-UGent) diff -ru EVidenceModeler.orig/Makefile EVidenceModeler/Makefile --- EVidenceModeler.orig/Makefile 2024-10-10 09:25:20.000000000 +0200 +++ EVidenceModeler/Makefile 2024-10-16 10:58:57.509308850 +0200 diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb index fd353611406..62454399723 100644 --- a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -21,7 +21,7 @@ sources = [{ patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] checksums = [ None, # EVidenceModeler-v2.1.0.tar.gz - '28eddb23ed39afcafb9c728d3951b089e70f3125b142119f036c48383550a738', + '619fc54db10fad3638daa177373c19c9ba4b69dcb80585822bfa9b2500f57d13', # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch ] From 01ea63a9a802ab9dc0ab7e43b68e7307ab53bc4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Oct 2024 10:27:03 +0200 Subject: [PATCH 274/524] {tools}[GCC/13.3.0] columba v1.2-20240326, sparsehash v2.0.4 --- .../columba-1.2-20240326-GCC-13.3.0.eb | 29 +++++++++++++++ .../sparsehash-2.0.4-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb b/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb new file mode 100644 index 00000000000..bbdb6d884b8 --- /dev/null +++ b/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'columba' +local_commit = '526b0a0' +version = '1.2-20240326' + +homepage = 'https://github.com/biointec/columba' +description = "Fast Approximate Pattern Matching using Search Schemes" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/biointec/columba/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['018898cf6ba93a974a141b397b68a7df13457e80bf92b1747f7b30c4a0d756f1'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('sparsehash', '2.0.4'), +] + +sanity_check_paths = { + 'files': ['bin/columba', 'bin/columba_build'], + 'dirs': [], +} + +sanity_check_commands = ["columba --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66056138103 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# Updated from previous easyconfig +# Author: Pavel Grochal (INUITS) +# Update: Pavel Tománek (INUITS) +# License: GPLv2 +# Updated to GCCcore-12.3.0 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.4' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' From fabe0442fa5404f8f49dca98995fa1bd9ce1c9bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Sat, 19 Oct 2024 12:36:35 +0200 Subject: [PATCH 275/524] adding easyconfigs: mpl-ascii-0.10.0-gfbf-2023b.eb --- .../mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb new file mode 100644 index 00000000000..f17a99eb068 --- /dev/null +++ b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpl-ascii' +version = '0.10.0' + +homepage = 'https://github.com/chriscave/mpl_ascii' +description = "A matplotlib backend that produces plots using only ASCII characters" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('matplotlib', '3.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'mpl_ascii-%(version)s.tar.gz', + 'checksums': ['8e4ae770d5a612dab0e8055c7677c6c3d271da4f5127cce46a60ce3ce4a4e72c'], + # relax version constraint for rich + 'preinstallopts': """sed -i 's/"rich>=.*"/"rich"/g' pyproject.toml && """, + }), +] + +moduleclass = 'vis' From b70a1bb747792d4799b2e2bb396d100dc62501ed Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 12:57:36 +0200 Subject: [PATCH 276/524] don't use name template in url --- easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb index c59f835b044..c19bcd1b72e 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb @@ -16,7 +16,7 @@ description = "Eigenvalue SoLvers for Petaflop-Applications." toolchain = {'name': 'foss', 'version': '2024a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://gitlab.mpcdf.mpg.de/%(namelower)s/%(namelower)s/-/archive/release_%(version)s/'] +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/release_%(version)s/'] sources = ['{}-release_{}.tar.gz'.format('%(namelower)s', local_version)] patches = [ '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', From 3ea7ca36e1483b749acd7c0fc8fb3430b9351157 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 13:05:46 +0200 Subject: [PATCH 277/524] use local_version in url --- easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb index c19bcd1b72e..8dcbc6ed3f2 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb @@ -16,7 +16,7 @@ description = "Eigenvalue SoLvers for Petaflop-Applications." toolchain = {'name': 'foss', 'version': '2024a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/release_%(version)s/'] +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/release_%s/' % local_version] sources = ['{}-release_{}.tar.gz'.format('%(namelower)s', local_version)] patches = [ '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', From 654c9a6a38c657899d7ebc59ae3b1e5f097a5f18 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 13:23:08 +0200 Subject: [PATCH 278/524] Update gperftools-2.16-GCCcore-13.3.0.eb --- .../g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb index b142fbdb34d..115b3754cff 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -12,6 +12,7 @@ Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +github_account = '%(name)s' source_urls = [GITHUB_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['737be182b4e42f5c7f595da2a7aa59ce0489a73d336d0d16847f2aa52d5221b4'] @@ -27,10 +28,9 @@ dependencies = [ preconfigopts = "autoreconf -f -i && " configopts = '--enable-libunwind' -github_account = '%(name)s' - -sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.so', 'lib/libtcmalloc.a', 'lib/libtcmalloc.so'], +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], 'dirs': ['include'], } From 11638b4b9cdeea4990cae51191be295f5cf21251 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 14:09:12 +0200 Subject: [PATCH 279/524] remove trailing whitespace --- .../easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb index 115b3754cff..1a31ffabd1b 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ preconfigopts = "autoreconf -f -i && " configopts = '--enable-libunwind' -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], 'dirs': ['include'], From 932949489b4af84c0b8497917b737588b94da3e3 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 14:44:09 +0200 Subject: [PATCH 280/524] don't use CMAKE_BUILD_TYPE=Release --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 9e1c986fa71..cc85303ac57 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -34,7 +34,6 @@ dependencies = [ build_type = 'Release' configopts = '-DCMAKE_CXX_COMPILER=g++ ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' configopts += '-DHPX_WITH_HWLOC=TRUE ' configopts += '-DHPX_WITH_GOOGLE_PERFTOOLS=TRUE ' From 9a016ef98b98c9b7071bd9d2c8b35b5b4e0f3612 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:24:18 +0200 Subject: [PATCH 281/524] change dependencies to resolve duplicates with different versions --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb index 6b10fd59155..688984aca59 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb @@ -35,7 +35,7 @@ builddependencies = [ # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile dependencies = [ ('Java', '11', '', SYSTEM), - ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), @@ -55,7 +55,7 @@ dependencies = [ ('RSEM', '1.3.3'), ('Salmon', '1.10.3'), ('SAMtools', '1.18'), - ('STAR', '2.7.11b'), + ('STAR', '2.7.11a'), ('zlib', '1.2.13'), ] From febfc467212019e5dd469ad14bc0193c7002a4dc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:26:43 +0200 Subject: [PATCH 282/524] change dependencies to resolve duplicates with different versions --- easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb index c3170802211..559d54704d5 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb @@ -40,7 +40,7 @@ dependencies = [ ('R', '4.3.2'), ('R-bundle-CRAN', '2023.12'), ('HISAT2', '2.2.1'), - ('STAR', '2.7.11b'), + ('STAR', '2.7.11a'), ('Bowtie2', '2.5.1'), ('Bowtie', '1.3.1'), ] From fad9256dbe02611fa81f29d2f837a5bdc1b9f64f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:29:38 +0200 Subject: [PATCH 283/524] change dependencies to resolve duplicates with different versions --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb new file mode 100644 index 00000000000..a2838a99654 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.2' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.5.1'), + ('GMAP-GSNAP', '2023-04-20'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.18'), + ('Jellyfish', '2.3.1'), + ('kallisto', '0.51.1'), + ('ncurses', '6.4'), + ('RSEM', '1.3.3'), + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('zlib', '1.2.13'), +] + +withsampledata = True + +moduleclass = 'bio' From cfe83af7e98c4a2a1519eda158b8b52b9e35e184 Mon Sep 17 00:00:00 2001 From: lara Date: Sat, 19 Oct 2024 22:34:19 +0200 Subject: [PATCH 284/524] remove old version of Trinity --- .../t/Trinity/Trinity-2.15.1-foss-2023a.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb deleted file mode 100644 index 688984aca59..00000000000 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb +++ /dev/null @@ -1,64 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -name = 'Trinity' -version = '2.15.1' - -homepage = 'https://trinityrnaseq.github.io' -description = """Trinity represents a novel method for the efficient and robust de novo reconstruction - of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, - Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] -sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] -patches = ['Trinity-%(version)s_fix-bamsifter.patch'] -checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, -] - -builddependencies = [ - ('Autotools', '20220317'), - ('CMake', '3.26.3'), -] - -# for reference, list of dependencies in the container image used upstream: -# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile -dependencies = [ - ('Java', '11', '', SYSTEM), - ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), - ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), - ('GATK', '4.3.0.0', '-Java-%(javaver)s'), - ('Perl', '5.36.1'), - ('Perl-bundle-CPAN', '5.36.1'), - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('BLAST+', '2.14.1'), - ('BLAT', '3.7'), - ('Bowtie', '1.3.1'), - ('Bowtie2', '2.5.1'), - ('GMAP-GSNAP', '2023-04-20'), - ('HISAT2', '2.2.1'), - ('HTSlib', '1.18'), - ('Jellyfish', '2.3.1'), - ('kallisto', '0.51.1'), - ('ncurses', '6.4'), - ('RSEM', '1.3.3'), - ('Salmon', '1.10.3'), - ('SAMtools', '1.18'), - ('STAR', '2.7.11a'), - ('zlib', '1.2.13'), -] - -withsampledata = True - -moduleclass = 'bio' From e1c227f47f987359105ac2746cef2257293638cf Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:36:56 +0200 Subject: [PATCH 285/524] change Trinity version --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index 22a735ac9af..0eeac174f28 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -21,7 +21,7 @@ dependencies = [ ('tbl2asn', '20230713', '-linux64', SYSTEM), ('DBD-mysql', '4.050'), ('CodingQuarry', '2.0'), - ('Trinity', '2.15.1'), + ('Trinity', '2.15.2'), ('AUGUSTUS', '3.5.0'), ('BamTools', '2.5.2'), ('BEDTools', '2.31.0'), From 68ce4bb3296a90a4ab52355a83a09738d17d9801 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 11:19:23 +0200 Subject: [PATCH 286/524] inject right checksums and change patch file for Trinity --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 4 ++-- .../Trinity/Trinity-2.15.2_fix-bamsifter.patch | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index a2838a99654..8ed7523a32f 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -22,8 +22,8 @@ source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch new file mode 100644 index 00000000000..508450dfb18 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -0,0 +1,17 @@ +Fix build of Trinity plugin bamsifter: +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) +--- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 ++++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 +@@ -2,8 +2,8 @@ + + cwd = $(shell pwd) + +-sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h +- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts ++sift_bam_max_cov: sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp + + + htslib/version.h : From b2e5c965f8970ef6b1b99078b6813dcffed16361 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 14:53:07 +0200 Subject: [PATCH 287/524] fix checksum --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 8ed7523a32f..147daa157b6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] builddependencies = [ From 59c8a5fc96e7a4802d4389e9d3076ed223780ae0 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 23:50:27 +0200 Subject: [PATCH 288/524] fix checksum --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 147daa157b6..7529d768672 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, + {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] From c10793a93f7516ea88755d0c65eefc0aa2b33d9e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 08:12:53 +0200 Subject: [PATCH 289/524] hopefully the patch and checksum drama ends with this one --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- .../t/Trinity/Trinity-2.15.2_fix-bamsifter.patch | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 7529d768672..c14b372365c 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'bcb35c45ffd82d3da073c4f768719c1e74786ec7810e8311c141a4ebffd48053'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch index 508450dfb18..f82c4126b99 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -1,9 +1,10 @@ Fix build of Trinity plugin bamsifter: -* use external HTSlib from EasyBuild environment -* use compilation flags from environment -author: Alex Domingo (Vrije Universiteit Brussel) ---- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 -+++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 + 2 * use external HTSlib from EasyBuild environment + 3 * use compilation flags from environment + 4 author: Alex Domingo (Vrije Universiteit Brussel) +diff -ru trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile +--- trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile 2024-08-01 14:53:23.000000000 +0200 ++++ trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile 2024-10-21 07:50:10.911559350 +0200 @@ -2,8 +2,8 @@ cwd = $(shell pwd) @@ -11,7 +12,7 @@ author: Alex Domingo (Vrije Universiteit Brussel) -sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h - g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts +sift_bam_max_cov: sift_bam_max_cov.cpp -+ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp htslib/version.h : From dd66bb63d3e16bf2ec5a47da39aad9146b84f882 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 08:16:30 +0200 Subject: [PATCH 290/524] hopefully the patch and checksum drama ends with this one --- .../t/Trinity/Trinity-2.15.2_fix-bamsifter.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch index f82c4126b99..9e414a414f1 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -1,7 +1,7 @@ Fix build of Trinity plugin bamsifter: - 2 * use external HTSlib from EasyBuild environment - 3 * use compilation flags from environment - 4 author: Alex Domingo (Vrije Universiteit Brussel) +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) diff -ru trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile --- trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile 2024-08-01 14:53:23.000000000 +0200 +++ trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile 2024-10-21 07:50:10.911559350 +0200 From 575af9e8b402afddeee0560be4da23d945fcd407 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 21 Oct 2024 09:21:51 +0000 Subject: [PATCH 291/524] adding easyconfigs: snptest-2.5.6.eb --- .../easyconfigs/s/snptest/snptest-2.5.6.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb diff --git a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb new file mode 100644 index 00000000000..8c1a46c08dc --- /dev/null +++ b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'snptest' +version = '2.5.6' + +homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' +description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. + The tests implemented include + + Binary (case-control) phenotypes, single and multiple quantitative phenotypes + Bayesian and Frequentist tests + Ability to condition upon an arbitrary set of covariates and/or SNPs. + Various different methods for the dealing with imputed SNPs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] +sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] +checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] + +sanity_check_paths = { + 'files': ['LICENCE'], + 'dirs': ['doc', 'example'], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ["snptest_v2.5.6 -help"] + +moduleclass = 'bio' From 9da9917445061757bc89d35af9b013973f437aa0 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 21 Oct 2024 12:52:55 +0200 Subject: [PATCH 292/524] Update easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index cc85303ac57..edc922f3056 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -31,8 +31,6 @@ dependencies = [ ('gperftools', '2.16'), ] -build_type = 'Release' - configopts = '-DCMAKE_CXX_COMPILER=g++ ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' configopts += '-DHPX_WITH_HWLOC=TRUE ' From 1359bc0ba1f6a5232fff16e2c32ddfad78d46eb7 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 14:08:55 +0200 Subject: [PATCH 293/524] hopefully the patch and checksum drama ends with this one --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index c14b372365c..8ecc76c588a 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.2_fix-bamsifter.patch': 'bcb35c45ffd82d3da073c4f768719c1e74786ec7810e8311c141a4ebffd48053'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'f557a3d462218e27f3601ac07edd2bbafe5fdb088ab81f642e7025edfe3e48ef'}, ] builddependencies = [ From c52d81dc6bf47759f6c89de9b8b5c71608ea2286 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 21 Oct 2024 15:20:03 +0200 Subject: [PATCH 294/524] adding easyconfigs: SciANN-0.7.0.1-foss-2022a.eb --- .../s/SciANN/SciANN-0.7.0.1-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb new file mode 100644 index 00000000000..0717fc8e997 --- /dev/null +++ b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'SciANN' +version = '0.7.0.1' + +homepage = 'https://github.com/ehsanhaghighat/sciann' +description = """ +A Keras/Tensorflow wrapper for scientific computations and physics-informed deep learning +using artificial neural networks. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('TensorFlow', '2.11.0'), + ('pymatgen', '2023.3.10'), # for pybtex and latexcodec + ('matplotlib', '3.5.2'), + ('pygraphviz', '1.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pydot', '2.0.0', { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), + (name, version, { + 'modulename': 'sciann', + 'checksums': ['7d7acf61346b4201628c5656e2c904e9a9c7cda78086e76d075b5c7bb90adf3c'], + }), +] + +moduleclass = 'ai' From 0f31ea0f359f895fb05ab51b95ff94fe3668ef11 Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 21 Oct 2024 16:18:04 +0200 Subject: [PATCH 295/524] adding easyconfigs: pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb --- .../pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..aceab404bda --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['cf8c669ffb0fda4cb594550fb233f9654252db50671b59147826eadc0a3d5565'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM) +] + +configopts = '-DPMT_BUILD_RAPL=1 -DPMT_BUILD_NVML=1 -DPMT_BUILD_NVIDIA=1' + +sanity_check_paths = { + 'files': ["lib/libpmt.so", "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' From d52cd0bc32e41a747e6f8fc2d65ec09f1652f8bb Mon Sep 17 00:00:00 2001 From: software Date: Mon, 21 Oct 2024 15:35:55 +0000 Subject: [PATCH 296/524] Use uppercase naming and add unversioned symlink to the binary --- .../easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb diff --git a/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb new file mode 100644 index 00000000000..a404d99e468 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'SNPTEST' +version = '2.5.6' + +homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' +description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. + The tests implemented include + + Binary (case-control) phenotypes, single and multiple quantitative phenotypes + Bayesian and Frequentist tests + Ability to condition upon an arbitrary set of covariates and/or SNPs. + Various different methods for the dealing with imputed SNPs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] +sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] +checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] + +postinstallcmds = ["cd %(installdir)s && ln -s snptest_v2.5.6 snptest"] + +sanity_check_paths = { + 'files': ['LICENCE'], + 'dirs': ['doc', 'example'], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ["snptest -help"] + +moduleclass = 'bio' From 3950c50851f9958fe0e619ae5190d274eb7a029b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 21 Oct 2024 16:38:47 +0100 Subject: [PATCH 297/524] Delete easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb --- .../easyconfigs/s/snptest/snptest-2.5.6.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb diff --git a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb b/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb deleted file mode 100644 index 8c1a46c08dc..00000000000 --- a/easybuild/easyconfigs/s/snptest/snptest-2.5.6.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'Tarball' - -name = 'snptest' -version = '2.5.6' - -homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' -description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. - The tests implemented include - - Binary (case-control) phenotypes, single and multiple quantitative phenotypes - Bayesian and Frequentist tests - Ability to condition upon an arbitrary set of covariates and/or SNPs. - Various different methods for the dealing with imputed SNPs. -""" - -toolchain = SYSTEM - -source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] -sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] -checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] - -sanity_check_paths = { - 'files': ['LICENCE'], - 'dirs': ['doc', 'example'], -} - -modextrapaths = {'PATH': ''} - -sanity_check_commands = ["snptest_v2.5.6 -help"] - -moduleclass = 'bio' From 091cfe5dade66635aea58a3c4e9090c4600bedec Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 21 Oct 2024 17:59:40 +0200 Subject: [PATCH 298/524] fix mpi include issue, see https://github.com/wannier-developers/wannier90/issues/521 --- .../w/Wannier90/Wannier90-3.1.0-foss-2023a.eb | 4 ++- .../w/Wannier90/Wannier90-3.1.0-foss-2024a.eb | 4 ++- .../Wannier90/Wannier90-3.1.0-gomkl-2023a.eb | 9 ++++--- .../Wannier90/Wannier90-3.1.0-intel-2023a.eb | 9 ++++--- .../Wannier90/Wannier90-3.1.0-intel-2024a.eb | 9 ++++--- .../Wannier90_3.1.0_fix_mpi_include.patch | 27 +++++++++++++++++++ 6 files changed, 51 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb index f8fe7f68bbf..57105d3bdb6 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb index 3228ba164b9..26e4b587a1f 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb index 336ac8a3895..a3e59ef46a9 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be @@ -25,10 +27,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb index cf258368771..eb71d75290d 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb @@ -12,20 +12,23 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb index dd30db79af6..34d3457ccc4 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb @@ -12,20 +12,23 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch new file mode 100644 index 00000000000..fdc859c8a7f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch @@ -0,0 +1,27 @@ +Use "use mpi" to load all required interfaces. +See https://github.com/wannier-developers/wannier90/issues/521 +Author: Stefan Wolfsheimer (SURF) + + +diff -ruN wannier90-3.1.0.orig/src/comms.F90 wannier90-3.1.0/src/comms.F90 +--- wannier90-3.1.0.orig/src/comms.F90 2020-03-05 19:41:10.000000000 +0100 ++++ wannier90-3.1.0/src/comms.F90 2024-10-21 17:01:00.542755184 +0200 +@@ -23,15 +23,13 @@ + + use w90_constants, only: dp + use w90_io, only: io_error +- ++#ifdef MPI ++ use mpi ++#endif + implicit none + + private + +-#ifdef MPI +- include 'mpif.h' +-#endif +- + logical, public, save :: on_root + !! Are we the root node + integer, public, save :: num_nodes From 61826702179fcba592e84e718a251a0a051bb19a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 21 Oct 2024 18:48:54 +0200 Subject: [PATCH 299/524] Improve snaity check part --- .../h/HPX/HPX-1.10.0-foss-2024a.eb | 28 +++++++++++++++++-- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index edc922f3056..07eeef3d446 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -46,11 +46,33 @@ configopts += '-DHPX_WITH_FETCH_ASIO=TRUE ' bin_lib_subdirs = ['lib/%(namelower)s/'] +local_lib_names = [ + 'libhpx_accumulator.%s' % SHLIB_EXT, + 'libhpx_cancelable_action.%s' % SHLIB_EXT, + 'libhpx_component_storage.%s' % SHLIB_EXT, + 'libhpx_core.%s' % SHLIB_EXT, + 'libhpx_iostreams.%s' % SHLIB_EXT, + 'libhpx_jacobi.%s' % SHLIB_EXT, + 'libhpx_nqueen.%s' % SHLIB_EXT, + 'libhpx_partitioned_vector.%s' % SHLIB_EXT, + 'libhpx_process.%s' % SHLIB_EXT, + 'libhpx_random_mem_access.%s' % SHLIB_EXT, + 'libhpx_simple_central_tuplespace.%s' % SHLIB_EXT, + 'libhpx.%s' % SHLIB_EXT, + 'libhpx_startup_shutdown.%s' % SHLIB_EXT, + 'libhpx_template_accumulator.%s' % SHLIB_EXT, + 'libhpx_template_function_accumulator.%s' % SHLIB_EXT, + 'libhpx_throttle.%s' % SHLIB_EXT, + 'libhpx_unordered.%s' % SHLIB_EXT, +] + sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib'], + 'files': ['lib/%s' % l for l in local_lib_names] + + ['include/asio.hpp', 'include/hpx/hpx.hpp'] + + ['bin/hpxcxx', 'bin/hpxrun.py'], + 'dirs': ['bin', 'lib'] + bin_lib_subdirs, } -modextrapaths = {'LD_LIBRARY_PATH': ['lib/%(namelower)s']} +modextrapaths = {'LD_LIBRARY_PATH': bin_lib_subdirs} moduleclass = 'math' From e2784cac2a4cb2d92bbe9de57181e958c2550065 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 21 Oct 2024 20:54:23 +0000 Subject: [PATCH 300/524] try adding unidist again --- .../easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5ed0e424dfd..68d20abb137 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -29,14 +29,15 @@ dependencies = [ use_pip = True exts_list = [ - # modin has another backend, "unidist", for MPI, but it seems broken currently. - # The unidist backend will just fire up all cores as if initializing but not actually advance. - # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path + ('unidist', '0.7.2', { + 'checksums': ['6386e1ad5143fe132b9f96e232fe85fc39830ed2886515440e4ba1473255e4a0'], + }), (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" - ), + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py " + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From e26dbceba35823e7d8a1382802575f8f52a8c59e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 21 Oct 2024 20:59:07 +0000 Subject: [PATCH 301/524] fix a typo --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 68d20abb137..d9239113e25 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -35,7 +35,7 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py " + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py && " "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', From f0f4e2433f6d48b23aab70c4dbdf79c785479df1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 21 Oct 2024 23:00:18 +0200 Subject: [PATCH 302/524] Fix stile --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 07eeef3d446..110ca403b7c 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -67,7 +67,7 @@ local_lib_names = [ ] sanity_check_paths = { - 'files': ['lib/%s' % l for l in local_lib_names] + + 'files': ['lib/%s' % lib for lib in local_lib_names] + ['include/asio.hpp', 'include/hpx/hpx.hpp'] + ['bin/hpxcxx', 'bin/hpxrun.py'], 'dirs': ['bin', 'lib'] + bin_lib_subdirs, From 7f55ef3d35ca7dd5df6fe1e855d8a3a18bd12c4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 22 Oct 2024 12:01:02 +0200 Subject: [PATCH 303/524] try the tests which are segfaulting on `donphan` --- easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb index cc48f534ee8..becc50b238e 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -31,9 +31,6 @@ dependencies = [ ('HDF5', '1.14.0'), ] -# disable tests ending up with SEGFAULT -preconfigopts = "sed -i '/back_spawn_excit_gen/d' '%(builddir)s/NECI_STABLE/unit_tests/CMakeLists.txt' && " - # enable support for HDF5 configopts = "-DENABLE_HDF5=ON" From 065333017730480123859eda539cf51741639d92 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 22 Oct 2024 10:20:07 +0000 Subject: [PATCH 304/524] fix unidist test? --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index d9239113e25..3d6ce8d2958 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -32,12 +32,15 @@ exts_list = [ ('unidist', '0.7.2', { 'checksums': ['6386e1ad5143fe132b9f96e232fe85fc39830ed2886515440e4ba1473255e4a0'], }), + # The oversubscription is done in their own CI as well. + # Ray has limitations on unix socket path length, so it is not tested here. (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py && " - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" - ), + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi " + "mpiexec -n=1 --map-by :OVERSUBSCRIBE pytest modin/tests/pandas/test_general.py &&" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From 490b6fa7d12b9a476c0e11b64ed786823aa4254c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 22 Oct 2024 15:48:08 +0200 Subject: [PATCH 305/524] adding easyconfigs: PyBioLib-1.2.205-GCCcore-12.3.0.eb --- .../PyBioLib-1.2.205-GCCcore-12.3.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fe4e8b0e393 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb @@ -0,0 +1,68 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.2.205' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Flask', '2.3.3'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('commonmark', '0.9.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['da2f38c92590f83de410ba1a3cbceafbc74fee9def35f9251ba9a971d6d66fd9'], + }), + ('rich', '13.9.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1'], + }), + ('pycryptodome', '3.21.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['f7787e0d469bdae763b876174cf2e6c0f7be79808af26b1da96f1a64bcf47297'], + }), + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526'], + }), + ('docker', '7.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0'], + }), + ('PyJWT', '2.9.0', { + 'modulename': 'jwt', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3b02fb0f44517787776cf48f2ae25d8e14f300e6d7545a4315cee571a415e850'], + }), + ('gunicorn', '23.0.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + # 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['56030cdeec254ac751b47dab4f9418caa0c8af3d2604cc2daaa5cea2ab61312a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 487740c25c6ecce63fe96bcd99ad20c8d8ccbb47 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 22 Oct 2024 16:57:57 +0200 Subject: [PATCH 306/524] Add NWchem for 2024a --- .../GlobalArrays-5.8.2-intel-2024a.eb | 30 ++++++++++++++++ .../n/NWChem/NWChem-7.2.3-intel-2024a.eb | 34 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb new file mode 100644 index 00000000000..40829149482 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(name)s/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb new file mode 100644 index 00000000000..7b3190a3cd4 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb @@ -0,0 +1,34 @@ +name = 'NWChem' +version = '7.2.3' + +homepage = 'https://nwchemgit.github.io/' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/archive/refs/tags/'] +sources = ['v%(version)s-release.tar.gz'] +patches = [ + 'NWChem-7.0.2_fix_gnumakefile.patch', +] +checksums = [ + {'v7.2.3-release.tar.gz': 'fec76fbe650cdab8b00c8c1d7a5671554313e04a8e9e2fb300a7aad486910e6f'}, + {'NWChem-7.0.2_fix_gnumakefile.patch': '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4'}, +] + +dependencies = [ + ('GlobalArrays', '5.8.2'), + ('Python', '3.12.3'), +] + +preconfigopts = "export EXTRA_LIBS=-lutil && " + +modules = "all python" + +moduleclass = 'chem' From dc8710c4bd7512f1a5cfca39d2be596181db23bd Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Oct 2024 17:23:11 +0200 Subject: [PATCH 307/524] adding easyconfigs: GSL-2.8-GCC-13.3.0.eb --- .../easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..251304ed936 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.8' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 42bf4d53f732286a61ead16586802156ca68546e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Oct 2024 18:39:40 +0200 Subject: [PATCH 308/524] adding easyconfigs: libepoxy-1.5.10-GCCcore-13.3.0.eb --- .../libepoxy-1.5.10-GCCcore-13.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bca992c268a --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('Mesa', '24.1.3'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From ae174c2c5fde948cafceeb097850fb4d68e7814c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 23 Oct 2024 00:06:57 +0200 Subject: [PATCH 309/524] GTK3-3.24.42-GCCcore-13.3.0.eb --- .../g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2df9a346d4a --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.42' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('cairo', '1.18.0'), + ('Gdk-Pixbuf', '2.42.11'), + ('GLib', '2.80.4'), + ('Pango', '1.54.0'), + ('libepoxy', '1.5.10'), + ('X11', '20240607'), + ('FriBidi', '1.0.15'), + ('Wayland', '1.23.0'), +] + +default_easyblock = 'MesonNinja' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['50f89f615092d4dd01bbd759719f8bd380e5f149f6fd78a94725e2de112377e2'], + }), + ('hicolor-icon-theme', '0.18', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['db0e50a80aa3bf64bb45cbca5cf9f75efd9348cf2ac690b907435238c3cf81d7'], + }), + ('adwaita-icon-theme', '47.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'checksums': ['ad088a22958cb8469e41d9f1bba0efb27e586a2102213cd89cc26db2e002bdfe'], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' From 0f6cb8bb397c7f0282f1636f4259905c66d7953b Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 23 Oct 2024 08:54:35 +0200 Subject: [PATCH 310/524] GStreamer-1.24.8 --- .../GST-plugins-base-1.24.8-GCC-13.3.0.eb | 43 +++++++++++++++++ .../GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb | 47 +++++++++++++++++++ .../GStreamer-1.24_fix_bad_suid.patch | 22 +++++++++ .../Graphene-1.10.8-GCCcore-13.3.0.eb | 32 +++++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..13311a9a434 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['10fb31743750ccd498d3933e8aaecda563ebc65596a6ab875b47ee936e4b9599'] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('GLib', '2.80.4'), + ('GStreamer', '1.24.8'), + ('Gdk-Pixbuf', '2.42.11'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..6b256f6e3df --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.freedesktop.org/src/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-1.24_fix_bad_suid.patch'] +checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', # gstreamer-1.24.8.tar.xz + 'e40c8b195cc9d44f2d9b92e57608e097ef8dac6fa761c5610fcb836f88610cb1', # %(name)s-1.24_fix_bad_suid.patch +] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Perl', '5.38.2'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('Python', '3.12.3'), + ('zlib', '1.3.1'), + ('GMP', '6.3.0'), + ('GSL', '2.8'), + ('GLib', '2.80.4'), + ('libunwind', '1.8.1'), + ('elfutils', '0.191'), +] + + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch new file mode 100644 index 00000000000..c7497079889 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch @@ -0,0 +1,22 @@ +Do NOT make files setuid or try to do setcap. +That's a recipe for disaster. +Åke Sandgren, 20221031 +Stefan Wolfsheimer, upated to version 1.24.8 + +--- gstreamer-1.24.8.orig/libs/gst/helpers/ptp/ptp_helper_post_install.sh 2024-09-19 12:01:21.000000000 +0200 ++++ gstreamer-1.24.8/libs/gst/helpers/ptp/ptp_helper_post_install.sh 2024-10-22 17:43:55.971711002 +0200 +@@ -11,14 +11,10 @@ + setuid-root) + echo "$0: permissions before: " + ls -l "$ptp_helper" +- chown root "$ptp_helper" || true +- chmod u+s "$ptp_helper" || true + echo "$0: permissions after: " + ls -l "$ptp_helper" + ;; + capabilities) +- echo "Calling $setcap cap_sys_nice,cap_net_bind_service,cap_net_admin+ep $ptp_helper" +- $setcap cap_sys_nice,cap_net_bind_service,cap_net_admin+ep "$ptp_helper" || true + ;; + none) + echo "No perms/caps to set for $ptp_helper" diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d2ff38adec0 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), + ('binutils', '2.42'), +] +dependencies = [('GLib', '2.80.4')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' From f68eb56342dc2bb022a00df10d3fcb860f3b2c0e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 23 Oct 2024 08:56:25 +0200 Subject: [PATCH 311/524] added wxWidgets --- .../w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb new file mode 100644 index 00000000000..0c9c8976770 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.6' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['939e5b77ddc5b6092d1d7d29491fe67010a2433cf9b9c0d841ee4d04acb9dce7'] + +builddependencies = [ + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('XZ', '5.4.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.6.0'), + ('expat', '2.6.2'), + ('GTK3', '3.24.42'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('SDL2', '2.30.6'), + ('cairo', '1.18.0'), + ('GST-plugins-base', '1.24.8'), + ('GLib', '2.80.4'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 3246954f059615c512b97a8cb5ed0a8ba85d2e52 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 23 Oct 2024 11:20:00 +0200 Subject: [PATCH 312/524] adding easyconfigs: modkit-0.3.3-GCCcore-12.3.0.eb --- .../m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb | 571 ++++++++++++++++++ 1 file changed, 571 insertions(+) create mode 100644 easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ad3a0522d39 --- /dev/null +++ b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,571 @@ +easyblock = 'Cargo' + +name = 'modkit' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/modkit' +description = 'A bioinformatics tool for working with modified bases.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nanoporetech/modkit/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +crates = [ + ('adler2', '2.0.0'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.91'), + ('approx', '0.5.1'), + ('arc-swap', '1.7.1'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.4.0'), + ('bio', '1.6.0'), + ('bio-types', '1.0.4'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '2.6.0'), + ('bitvec', '1.0.1'), + ('block-buffer', '0.10.4'), + ('bstr', '1.10.0'), + ('bumpalo', '3.16.0'), + ('bv', '0.11.1'), + ('bytecount', '0.6.8'), + ('bytemuck', '1.19.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.8.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.31'), + ('cfg-if', '1.0.0'), + ('charming', '0.3.1'), + ('chrono', '0.4.38'), + ('clap', '4.5.20'), + ('clap_builder', '4.5.20'), + ('clap_derive', '4.5.18'), + ('clap_lex', '0.7.2'), + ('cmake', '0.1.51'), + ('colorchoice', '1.0.2'), + ('common_macros', '0.1.1'), + ('console', '0.15.8'), + ('core-foundation-sys', '0.8.7'), + ('cpufeatures', '0.2.14'), + ('crc32fast', '1.4.2'), + ('crossbeam', '0.8.4'), + ('crossbeam-channel', '0.5.13'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-queue', '0.3.11'), + ('crossbeam-utils', '0.8.20'), + ('crypto-common', '0.1.6'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('curl-sys', '0.4.77+curl-8.10.1'), + ('custom_derive', '0.1.7'), + ('derivative', '2.2.0'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('destructure_traitobject', '0.2.0'), + ('digest', '0.10.7'), + ('dirs-next', '2.0.0'), + ('dirs-sys-next', '0.1.2'), + ('doc-comment', '0.3.3'), + ('editdistancek', '1.0.2'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('encode_unicode', '1.0.0'), + ('enum-map', '2.7.3'), + ('enum-map-derive', '0.17.0'), + ('equivalent', '1.0.1'), + ('errno', '0.3.9'), + ('fastrand', '2.1.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.34'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('funty', '2.0.0'), + ('fxhash', '0.2.1'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('handlebars', '4.5.0'), + ('hashbrown', '0.13.2'), + ('hashbrown', '0.15.0'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.3.9'), + ('hermit-abi', '0.4.0'), + ('hts-sys', '2.1.4'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.61'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '2.6.0'), + ('indicatif', '0.17.8'), + ('instant', '0.1.13'), + ('is-terminal', '0.4.13'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.11.0'), + ('itertools', '0.12.1'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.72'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.161'), + ('libm', '0.2.8'), + ('libredox', '0.1.3'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('log-mdc', '0.1.0'), + ('log-once', '0.4.1'), + ('log4rs', '1.3.0'), + ('lru', '0.9.0'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.9'), + ('memchr', '2.7.4'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.8.0'), + ('multimap', '0.9.1'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('newtype_derive', '0.1.6'), + ('nom', '7.1.3'), + ('noodles', '0.50.0'), + ('noodles-bgzf', '0.24.0'), + ('noodles-core', 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'589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'wyz-0.5.1.tar.gz': '05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +moduleclass = 'bio' From 7254e425e521b362b305ca91b4d00b02841d9ca3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 23 Oct 2024 11:23:31 +0200 Subject: [PATCH 313/524] adding easyconfigs: modkit-0.4.1-GCCcore-13.3.0.eb --- .../m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb | 585 ++++++++++++++++++ 1 file changed, 585 insertions(+) create mode 100644 easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4899fba40e5 --- /dev/null +++ b/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,585 @@ +easyblock = 'Cargo' + +name = 'modkit' +version = '0.4.1' + +homepage = 'https://github.com/nanoporetech/modkit' +description = 'A bioinformatics tool for working with modified bases.' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/nanoporetech/modkit/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.42'), + ('Rust', '1.78.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +crates = [ + ('adler2', '2.0.0'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.90'), + ('approx', 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{'unicode-width-0.1.14.tar.gz': '7dd6e30e90baa6f72411720665d41d89b9a3d039dc45b8faea1ddd07f617f6af'}, + {'unsafe-any-ors-1.0.0.tar.gz': 'e0a303d30665362d9680d7d91d78b23f5f899504d4f08b3c4cf08d055d87c0ad'}, + {'unsafe-libyaml-0.2.11.tar.gz': '673aac59facbab8a9007c7f6108d11f63b603f7cabff99fabf650fea5c32b861'}, + {'url-2.5.2.tar.gz': '22784dbdf76fdde8af1aeda5622b546b422b6fc585325248a2bf9f5e41e94d6c'}, + {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'vec_map-0.8.2.tar.gz': 'f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191'}, + {'version_check-0.9.5.tar.gz': '0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wasm-bindgen-0.2.95.tar.gz': '128d1e363af62632b8eb57219c8fd7877144af57558fb2ef0368d0087bddeb2e'}, + {'wasm-bindgen-backend-0.2.95.tar.gz': 'cb6dd4d3ca0ddffd1dd1c9c04f94b868c37ff5fac97c30b97cff2d74fce3a358'}, + {'wasm-bindgen-macro-0.2.95.tar.gz': 'e79384be7f8f5a9dd5d7167216f022090cf1f9ec128e6e6a482a2cb5c5422c56'}, + {'wasm-bindgen-macro-support-0.2.95.tar.gz': '26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68'}, + {'wasm-bindgen-shared-0.2.95.tar.gz': '65fc09f10666a9f147042251e0dda9c18f166ff7de300607007e96bdebc1068d'}, + {'wide-0.7.28.tar.gz': 'b828f995bf1e9622031f8009f8481a85406ce1f4d4588ff746d872043e855690'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-core-0.52.0.tar.gz': '33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'wyz-0.5.1.tar.gz': '05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +moduleclass = 'bio' From 5890289f3584a0618432f93dd30da777bc23363b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 23 Oct 2024 15:47:05 +0200 Subject: [PATCH 314/524] adding easyconfigs: Dask-ML-2024.4.4-foss-2023a.eb --- .../d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb new file mode 100644 index 00000000000..9ff4d7c1b9c --- /dev/null +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Dask-ML' +version = '2024.4.4' + +homepage = 'http://ml.dask.org/' +description = """ +Dask-ML provides scalable machine learning in Python using Dask alongside popular machine +learning libraries like Scikit-Learn, XGBoost, and others. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('dask', '2023.9.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools-scm', '8.1.0', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), # sparse needs setuptools-scm>=8 + ('sparse', '0.15.4', { + 'checksums': ['d4b1c57d24ff0f64f2fd5b5a95b49b7fb84ed207a26d7d58ce2764dcc5c72b84'], + }), + ('dask-glm', '0.3.2', { + 'checksums': ['c947a566866698a01d79978ae73233cb5e838ad5ead6085143582c5e930b9a4a'], + }), + ('distributed', '2023.9.2', { + 'checksums': ['b76b43be6a297c6cc6dc4eac7f5a05a8c6834aaf025ed37395d1d830448d540e'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + (name, version, { + 'modulename': 'dask_ml', + 'sources': ['dask_ml-%(version)s.tar.gz'], + 'checksums': ['7956910a49e1e31944280fdb311adf245da11ef410d67deb7a05c67c7d0c4498'], + }), +] + +moduleclass = 'ai' From df78ba5261c08e697b328c9ddf069b7bcbd7ed69 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Oct 2024 16:11:00 +0200 Subject: [PATCH 315/524] adding easyconfigs: JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb --- ...SA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..7d67673eeae --- /dev/null +++ b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'JACUSA2helper' +version = '1.9.9.9675' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://dieterich-lab.github.io/JACUSA2helper/' +description = "Auxiliary R package for assessment of JACUSA2 results" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/dieterich-lab/JACUSA2helper/archive/refs/tags/'], + 'sources': 'v%(version)s.tar.gz', + 'checksums': ['5c8edb96a5691c7fb2895e50eb992ebe375f8d97234039da3f5540a7a9cb4816'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(%(name)s)"'] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 9cd879a0f46fe08dfae03fa2e74486f5e8b2252c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Oct 2024 16:15:23 +0200 Subject: [PATCH 316/524] remove versionsuffix --- .../JACUSA2helper-1.9.9.9675-foss-2023a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb diff --git a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb new file mode 100644 index 00000000000..7fbd1aae7e2 --- /dev/null +++ b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'JACUSA2helper' +version = '1.9.9.9675' + +homepage = 'https://dieterich-lab.github.io/JACUSA2helper/' +description = "Auxiliary R package for assessment of JACUSA2 results" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/dieterich-lab/JACUSA2helper/archive/refs/tags/'], + 'sources': 'v%(version)s.tar.gz', + 'checksums': ['5c8edb96a5691c7fb2895e50eb992ebe375f8d97234039da3f5540a7a9cb4816'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(%(name)s)"'] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 086b47a4c539721391f5ff027f4dc03b7a19a7c7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Oct 2024 16:50:42 +0200 Subject: [PATCH 317/524] use source_tmpl instead of sources for extension --- .../j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb index 7fbd1aae7e2..4b3003c89ec 100644 --- a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb +++ b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb @@ -19,7 +19,7 @@ exts_defaultclass = 'RPackage' exts_list = [ (name, version, { 'source_urls': ['https://github.com/dieterich-lab/JACUSA2helper/archive/refs/tags/'], - 'sources': 'v%(version)s.tar.gz', + 'source_tmpl': 'v%(version)s.tar.gz', 'checksums': ['5c8edb96a5691c7fb2895e50eb992ebe375f8d97234039da3f5540a7a9cb4816'], }), ] From 5fa5481d8fb1198bd458a5f35255a1242edc4dd2 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 23 Oct 2024 16:54:03 +0200 Subject: [PATCH 318/524] delete stale easyconfig --- ...SA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb deleted file mode 100644 index 7d67673eeae..00000000000 --- a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a-R-4.3.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'Bundle' - -name = 'JACUSA2helper' -version = '1.9.9.9675' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://dieterich-lab.github.io/JACUSA2helper/' -description = "Auxiliary R package for assessment of JACUSA2 results" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('R', '4.3.2'), - ('R-bundle-CRAN', '2023.12'), - ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), -] - -exts_defaultclass = 'RPackage' - -exts_list = [ - (name, version, { - 'source_urls': ['https://github.com/dieterich-lab/JACUSA2helper/archive/refs/tags/'], - 'sources': 'v%(version)s.tar.gz', - 'checksums': ['5c8edb96a5691c7fb2895e50eb992ebe375f8d97234039da3f5540a7a9cb4816'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -sanity_check_commands = ['Rscript -e "library(%(name)s)"'] - -modextrapaths = {'R_LIBS_SITE': ''} - -moduleclass = 'bio' From 9a217e15a8b6031eb070e98899f418a960babea3 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 23 Oct 2024 17:15:02 +0200 Subject: [PATCH 319/524] adding easyconfigs: Dask-ML-2022.5.27-foss-2022a.eb --- .../d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb new file mode 100644 index 00000000000..12884bd5e3a --- /dev/null +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Dask-ML' +version = '2022.5.27' + +homepage = 'http://ml.dask.org/' +description = """ +Dask-ML provides scalable machine learning in Python using Dask alongside popular machine +learning libraries like Scikit-Learn, XGBoost, and others. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('scikit-learn', '1.1.2'), + ('dask', '2022.10.0'), + ('numba', '0.56.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.14.0', { + 'checksums': ['5f5827a37f6cd6f6730a541f994c95c60a3ae2329e01f4ba21ced5339aea0098'], + }), + ('dask-glm', '0.3.2', { + 'checksums': ['c947a566866698a01d79978ae73233cb5e838ad5ead6085143582c5e930b9a4a'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('distributed', '2022.10.0', { + 'checksums': ['dcfbc9c528bcd9e4f9686e673956a90172826395ac5b258039e580777d50782f'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + (name, version, { + 'modulename': 'dask_ml', + 'sources': ['dask-ml-%(version)s.tar.gz'], + 'checksums': ['6369d3934192bcc1923fcee84c3fb8fbcceca102137901070ba3f1d9e386cce4'], + }), +] + +moduleclass = 'ai' From 40d39f50dea81c6268e51fe9ed1407529eaaf4aa Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 23 Oct 2024 17:41:43 +0200 Subject: [PATCH 320/524] Add NAMD and deps --- .../n/NAMD/NAMD-3.0-foss-2024a-mpi.eb | 35 ++++++++++++ .../n/NAMD/NAMD-3.0_fix_hwloc_build.patch | 54 +++++++++++++++++++ .../t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb | 48 +++++++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb new file mode 100644 index 00000000000..09c315d4561 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb @@ -0,0 +1,35 @@ +name = 'NAMD' +version = '3.0' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/946183/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] + +patches = ['NAMD-3.0_fix_hwloc_build.patch'] + +checksums = [ + '301c64f0f1db860f7336efdb26223ccf66b5ab42bfc9141df8d81ec1e20bf472', # NAMD_3.0_Source.tar.gz + '03f7caa4027604e0483a9b149ebb5de310653a2aad99403faf3359ccc0015f02', # NAMD-3.0_fix_hwloc_build.patch +] + +# /bin/csh is required by 'config' script +builddependencies = [ + ('tcsh', '6.24.13'), + ('Autotools', '20231222'), +] +dependencies = [ + ('Tcl', '8.6.14'), +] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try +charm_arch = 'mpi-linux-%(arch)s' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch b/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch new file mode 100644 index 00000000000..4b6683cf226 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch @@ -0,0 +1,54 @@ +# What: Fix hwloc cmake build issue in charm-8.0.0, see https://github.com/charmplusplus/charm/issues/3843 +# This patch is based on the following PR: https://github.com/charmplusplus/charm/pull/3847 +# Author: maxim-masterov (SURF) +diff -Nru NAMD_3.0_Source.orig/charm-8.0.0/contrib/hwloc/config/hwloc.m4 NAMD_3.0_Source/charm-8.0.0/contrib/hwloc/config/hwloc.m4 +--- NAMD_3.0_Source.orig/charm-8.0.0/contrib/hwloc/config/hwloc.m4 2024-10-02 14:22:40.779651616 +0200 ++++ NAMD_3.0_Source/charm-8.0.0/contrib/hwloc/config/hwloc.m4 2024-10-23 17:15:35.921883766 +0200 +@@ -140,28 +140,43 @@ + AC_CONFIG_HEADERS(hwloc_config_prefix[include/private/autogen/config.h]) + AC_CONFIG_HEADERS(hwloc_config_prefix[include/hwloc/autogen/config.h]) + ++ + # What prefix are we using? +- AC_MSG_CHECKING([for hwloc symbol prefix]) ++ AH_VERBATIM([prefix_details_ifndef], ++ [ /* hwloc details should only be set once */ ++ #ifndef HWLOC_SYM_DETAILS ++ #define HWLOC_SYM_DETAILS ++ ]) ++ AC_MSG_CHECKING([for hwloc symbol prefix]) + AS_IF([test "$hwloc_symbol_prefix_value" = ""], + [AS_IF([test "$with_hwloc_symbol_prefix" = ""], + [hwloc_symbol_prefix_value=hwloc_], + [hwloc_symbol_prefix_value=$with_hwloc_symbol_prefix])]) ++ ++ + AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX, [$hwloc_symbol_prefix_value], + [The hwloc symbol prefix]) + # Ensure to [] escape the whole next line so that we can get the + # proper tr tokens + [hwloc_symbol_prefix_value_caps="`echo $hwloc_symbol_prefix_value | tr '[:lower:]' '[:upper:]'`"] +- AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX_CAPS, [$hwloc_symbol_prefix_value_caps], +- [The hwloc symbol prefix in all caps]) ++ AC_CHECK_DEFINE([HWLOC_SYM_PREFIX_CAPS],[0],AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX_CAPS, [$hwloc_symbol_prefix_value_caps], ++ [The hwloc symbol prefix in all caps])) + AC_MSG_RESULT([$hwloc_symbol_prefix_value]) + +- # Give an easy #define to know if we need to transform all the ++ ++ # Give an easy #define to know if we need to transform all the + # hwloc names + AH_TEMPLATE([HWLOC_SYM_TRANSFORM], [Whether we need to re-define all the hwloc public symbols or not]) + AS_IF([test "$hwloc_symbol_prefix_value" = "hwloc_"], + [AC_DEFINE([HWLOC_SYM_TRANSFORM], [0])], + [AC_DEFINE([HWLOC_SYM_TRANSFORM], [1])]) + ++ AH_VERBATIM([prefix_details_endif], ++ [ /* HWLOC_DETAILS_SET */ ++ #endif ++ ]) ++ ++ + # Disabled for Charm++ due to https://github.com/charmplusplus/charm/issues/2606 + # hwloc 2.0+ requires a C99 compliant compiler + # AC_PROG_CC_C99 obsolete, detected inside AC_PROG_CC, since autoconf 2.70 diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a7712f10368 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +# # +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.13' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1e927d52e9c85d162bf985f24d13c6ccede9beb880d86fec492ed15480a5c71a'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), +] + +postinstallcmds = ['ln -s %(name)s %(installdir)s/bin/csh'] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/csh'], + 'dirs': [], +} + +moduleclass = 'tools' From e75f5985718e06932c820f3112d5d2afa175b7a7 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 23 Oct 2024 18:23:24 +0200 Subject: [PATCH 321/524] Add PRSice --- .../p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb | 44 ++++ .../p/PRSice/PRSice-2.3.5_remove_sysctl.patch | 194 ++++++++++++++++++ 2 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..85f8b20972c --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.5' + +homepage = 'https://choishingwan.github.io/PRSice/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/choishingwan/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['PRSice-2.3.5_remove_sysctl.patch'] +checksums = [ + '0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d', # 2.3.5.tar.gz + 'ab8286e8a0700ea163f552de66458e409c396e06b57c9adfff3b7f63083f7798', # PRSice-2.3.5_remove_sysctl.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('Eigen', '3.4.0'), +] + +files_to_copy = [ + (['bin/%(name)s'], 'bin'), + 'README.md', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch new file mode 100644 index 00000000000..04a71e26a8b --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch @@ -0,0 +1,194 @@ +# What: sysctl.h is removed in glibc v2.32. This patch is based on the following commits +# from https://github.com/choishingwan/PRSice: +# f285b243856b857a461d9a2b27e1f2f0ac25216e +# 53641c11750a7e0bdd06a925fbf28c1e3978ee72 +# Also see issue https://github.com/choishingwan/PRSice/issues/338 and PR https://github.com/choishingwan/PRSice/pull/243 +# Author: maxim-masterov (SURF) + +diff -Nru PRSice-2.3.5.orig/inc/misc.hpp PRSice-2.3.5/inc/misc.hpp +--- PRSice-2.3.5.orig/inc/misc.hpp 2024-10-23 18:13:58.539539000 +0200 ++++ PRSice-2.3.5/inc/misc.hpp 2024-10-23 18:14:29.383991502 +0200 +@@ -38,7 +38,6 @@ + #include + #include + #include +-#include + #elif defined _WIN32 + #include + // psapi must go after windows, or will generate error +@@ -48,7 +47,6 @@ + #include "stdlib.h" + #include "string.h" + #include +-#include + #include + #include + #endif +@@ -86,9 +84,6 @@ + #include + #include + #include +-#if defined(BSD) +-#include +-#endif + + #else + #error "Unable to define getMemorySize( ) for an unknown OS." +@@ -170,73 +165,7 @@ + // TODO: Delete this, doesn't seems to give robust answer + inline size_t current_ram_usage() { return 0; } + // TODO: Delete this, doesn't seems to give robust answer +-inline size_t total_ram_available() +-{ +-#ifdef __APPLE__ +- int32_t mib[2]; +- size_t sztmp; +-#endif +- unsigned char* bigstack_ua = nullptr; // ua = unaligned +- int64_t llxx; +- intptr_t default_alloc_mb; +- intptr_t malloc_size_mb = 0; +-#ifdef __APPLE__ +- mib[0] = CTL_HW; +- mib[1] = HW_MEMSIZE; +- llxx = 0; +- +- sztmp = sizeof(int64_t); +- sysctl(mib, 2, &llxx, &sztmp, nullptr, 0); +- llxx /= 1048576; +-#else +-#ifdef _WIN32 +- MEMORYSTATUSEX memstatus; +- memstatus.dwLength = sizeof(memstatus); +- GlobalMemoryStatusEx(&memstatus); +- llxx = memstatus.ullTotalPhys / 1048576; +-#else +- llxx = ((uint64_t) sysconf(_SC_PHYS_PAGES)) +- * ((size_t) sysconf(_SC_PAGESIZE)) / 1048576; +-#endif +-#endif +- if (!llxx) { default_alloc_mb = BIGSTACK_DEFAULT_MB; } +- else if (llxx < (BIGSTACK_MIN_MB * 2)) +- { +- default_alloc_mb = BIGSTACK_MIN_MB; +- } +- else +- { +- default_alloc_mb = llxx / 2; +- } +- if (!malloc_size_mb) { malloc_size_mb = default_alloc_mb; } +- else if (malloc_size_mb < BIGSTACK_MIN_MB) +- { +- malloc_size_mb = BIGSTACK_MIN_MB; +- } +- std::string message = ""; +-#ifndef __LP64__ +- if (malloc_size_mb > 2047) { malloc_size_mb = 2047; } +-#endif +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- // if fail, return nullptr which will then get into the while loop +- while (!bigstack_ua) +- { +- malloc_size_mb = (malloc_size_mb * 3) / 4; +- if (malloc_size_mb < BIGSTACK_MIN_MB) +- { malloc_size_mb = BIGSTACK_MIN_MB; } +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- if (bigstack_ua) {} +- else if (malloc_size_mb == BIGSTACK_MIN_MB) +- { +- throw std::runtime_error("Failed to allocate required memory"); +- } +- } +- free(bigstack_ua); +- bigstack_ua = nullptr; +- return malloc_size_mb * 1024 * 1024; +-} ++ + // function from John D.Cook + // https://www.johndcook.com/blog/standard_deviation/ + class RunningStat +@@ -1398,82 +1327,5 @@ + return (size_t) 0L; /* Unsupported. */ + #endif + } +- +- +-/** +- * Returns the size of physical memory (RAM) in bytes. +- */ +-inline size_t getMemorySize() +-{ +-#if defined(_WIN32) && (defined(__CYGWIN__) || defined(__CYGWIN32__)) +- /* Cygwin under Windows. ------------------------------------ */ +- /* New 64-bit MEMORYSTATUSEX isn't available. Use old 32.bit */ +- MEMORYSTATUS status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatus(&status); +- return (size_t) status.dwTotalPhys; +- +-#elif defined(_WIN32) +- /* Windows. ------------------------------------------------- */ +- /* Use new 64-bit MEMORYSTATUSEX, not old 32-bit MEMORYSTATUS */ +- MEMORYSTATUSEX status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatusEx(&status); +- return (size_t) status.ullTotalPhys; +- +-#elif defined(__unix__) || defined(__unix) || defined(unix) \ +- || (defined(__APPLE__) && defined(__MACH__)) +- /* UNIX variants. ------------------------------------------- */ +- /* Prefer sysctl() over sysconf() except sysctl() HW_REALMEM and HW_PHYSMEM +- */ +- +-#if defined(CTL_HW) && (defined(HW_MEMSIZE) || defined(HW_PHYSMEM64)) +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_MEMSIZE) +- mib[1] = HW_MEMSIZE; /* OSX. --------------------- */ +-#elif defined(HW_PHYSMEM64) +- mib[1] = HW_PHYSMEM64; /* NetBSD, OpenBSD. --------- */ +-#endif +- int64_t size = 0; /* 64-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +- +-#elif defined(_SC_AIX_REALMEM) +- /* AIX. ----------------------------------------------------- */ +- return (size_t) sysconf(_SC_AIX_REALMEM) * (size_t) 1024L; +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE) +- /* FreeBSD, Linux, OpenBSD, and Solaris. -------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGESIZE); +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGE_SIZE) +- /* Legacy. -------------------------------------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGE_SIZE); +- +-#elif defined(CTL_HW) && (defined(HW_PHYSMEM) || defined(HW_REALMEM)) +- /* DragonFly BSD, FreeBSD, NetBSD, OpenBSD, and OSX. -------- */ +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_REALMEM) +- mib[1] = HW_REALMEM; /* FreeBSD. ----------------- */ +-#elif defined(HW_PYSMEM) +- mib[1] = HW_PHYSMEM; /* Others. ------------------ */ +-#endif +- unsigned int size = 0; /* 32-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +-#endif /* sysctl and sysconf variants */ +- +-#else +- return 0L; /* Unknown OS. */ +-#endif + } + +-inline unsigned long long remain_memory(const double& adjFactor = 0.8) +-{ +- return (misc::getMemorySize() * adjFactor - getCurrentRSS()); +-} +-} From e4f088c3ef8cf7b42f098179c8f9e7b652a915de Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 23 Oct 2024 18:29:56 +0200 Subject: [PATCH 322/524] adding easyconfigs: SciKeras-0.12.0-foss-2022a.eb --- .../s/SciKeras/SciKeras-0.12.0-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb new file mode 100644 index 00000000000..ef229b6885b --- /dev/null +++ b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'SciKeras' +version = '0.12.0' + +homepage = 'https://adriangb.com/scikeras' +description = """ +Scikit-Learn API wrapper for Keras. The goal of scikeras is to make it possible to use +Keras/TensorFlow with sklearn. This is achieved by providing a wrapper around Keras that has +an Scikit-Learn interface. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('scikit-learn', '1.1.2'), + ('TensorFlow', '2.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'scikeras', + 'sources': ['scikeras-%(version)s.tar.gz'], + 'checksums': ['f60d81255a8904671bd33cbff060926cfa5ddd52fa234b12290afe3cb69dcc6c'], + }), +] + +moduleclass = 'ai' From 45aadd9b6883717fc743de39792960fa99b80f73 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 24 Oct 2024 11:41:40 +0200 Subject: [PATCH 323/524] adding easyconfigs: ReFrame-4.6.3-GCCcore-13.3.0.eb --- .../r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6541b14b799 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.3' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('cURL', '8.7.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.12.3'), + ('libxslt', '1.1.42'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.12.7'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['0f335e588d21a26d76beb011bc86baf80ba633d875512ecd564d0aeb320fcf2c'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' From 563bfd8bdd1b3aa21d20665688e9bec5ad946cec Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 24 Oct 2024 13:34:55 +0200 Subject: [PATCH 324/524] adding easyconfigs: ncdu-1.20-GCC-13.3.0.eb --- .../n/ncdu/ncdu-1.20-GCC-13.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb new file mode 100644 index 00000000000..e8f91407acf --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.20' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['5fe2bb841abe72374bb242dbb93293c4ae053078432d896a7481b2ff10be9572'] + +dependencies = [ + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From 2ec7b67caed14a20b247029184824b77a2024a11 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 24 Oct 2024 14:19:50 +0200 Subject: [PATCH 325/524] Add BEDTools and deps --- .../b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb | 53 +++++++++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb | 22 ++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..6bcbf918ae0 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb @@ -0,0 +1,53 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.1' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e'] + +builddependencies = [ + ('Python', '3.12.3'), +] +dependencies = [ + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [ + 'bin', + 'docs', + 'data', + 'genomes', + 'scripts', + 'test', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/pairToBed', 'bin/mergeBed', 'bin/bedToBam', 'bin/fastaFromBed'], + 'dirs': ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..23e1ad0e743 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' + +moduleclass = 'bio' From 682faee69e7ebe3583c235f5acc42be30ead319c Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 24 Oct 2024 15:58:33 +0200 Subject: [PATCH 326/524] update sanity check in GEOS-3.12.2-GCC-13.3.0.eb --- easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb index 839a0000216..6b174f0bf8a 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb @@ -19,7 +19,8 @@ builddependencies = [('CMake', '3.29.3')] configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { - 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos_c.so', 'include/geos.h'], + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'lib/libgeos_c.%s' % SHLIB_EXT, + 'include/geos.h'], 'dirs': [], } From d73399982f11233bff15b4c994d39cd4ef2ee6ec Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 24 Oct 2024 16:41:31 +0200 Subject: [PATCH 327/524] get sources from github --- .../t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb index a9c9fa5f5c4..107e7dbb9c9 100644 --- a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb @@ -9,9 +9,9 @@ description = """tRNAscan-SE is the most widely employed tool for identifying toolchain = {'name': 'foss', 'version': '2023a'} -source_urls = ['http://trna.ucsc.edu/software/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] +source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61'] builddependencies = [ # tRNAscan-SE's configure script really wants Autoconf 2.69 From 082043bc81e489637abab49303a5246c9f897aef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Oct 2024 17:14:38 +0200 Subject: [PATCH 328/524] {bio}[gompi/2023a] MEME v5.5.7, XML-Compile v1.63, XML-LibXML v2.0210 --- .../m/MEME/MEME-5.5.7-gompi-2023b.eb | 63 ++++++++++++++++++ .../XML-Compile-1.63-GCCcore-13.2.0.eb | 61 +++++++++++++++++ .../XML-LibXML-2.0210-GCCcore-13.2.0.eb | 65 +++++++++++++++++++ 3 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb new file mode 100644 index 00000000000..08fdaab9f31 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb @@ -0,0 +1,63 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.5.7' + +homepage = 'https://meme-suite.org/meme/index.html' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1dca8d0e6d1d36570c1a88ab8dbe7e4b177733fbbeacaa2e8c4674febf57aaf4'] + +dependencies = [ + ('libxml2', '2.11.5'), + ('libxslt', '1.1.38'), + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('Ghostscript', '10.02.1'), + ('XML-Compile', '1.63'), +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' +configopts += '--with-gs=${EBROOTGHOSTSCRIPT}/bin/gs ' +# config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) +configopts += " && grep 'All required and optional Perl modules were found' config.log" + +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +# test xstreme4 fails on Ubuntu 20.04, see: https://groups.google.com/g/meme-suite/c/GlfpGwApz1Y +runtest = 'test' + +fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] +fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] + +sanity_check_paths = { + 'files': ['bin/meme', 'bin/dreme', 'bin/meme-chip', 'libexec/meme-%(version)s/meme2meme'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "mpirun meme -h 2>&1 | grep 'Usage:'", + "meme2meme --help", + "perl -e 'require MemeSAX'", + "python -c 'import sequence_py3'", +] + +modextrapaths = { + 'PATH': ['libexec/meme-%(version)s'], + 'PERL5LIB': ['lib/meme-%(version)s/perl'], + 'PYTHONPATH': ['lib/meme-%(version)s/python'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7c564210edb --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'Bundle' + +name = 'XML-Compile' +version = '1.63' + +homepage = 'https://metacpan.org/pod/XML::Compile' +description = "Perl module for compilation based XML processing" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('XML-LibXML', '2.0210'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('XML::LibXML::Simple', '1.01', { + 'source_tmpl': 'XML-LibXML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['cd98c8104b70d7672bfa26b4513b78adf2b4b9220e586aa8beb1a508500365a6'], + }), + ('XML::Compile', version, { + 'source_tmpl': 'XML-Compile-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['4b0871ef4a70bff37266d531bebcd1d065b109e8f5c5e996f87189a9f92d595f'], + }), + ('XML::Compile::Cache', '1.06', { + 'source_tmpl': 'XML-Compile-Cache-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['591b136bd92842c81a5176082503f47df6d5cc4d8e0d78953ef1557f747038a0'], + }), + ('XML::Compile::SOAP', '3.28', { + 'source_tmpl': 'XML-Compile-SOAP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['0921699c4522537f7930e14fac056492de7801a9b9140d0e1faf33414ae6998f'], + }), + ('XML::Compile::WSDL11', '3.08', { + 'source_tmpl': 'XML-Compile-WSDL11-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['dd687ccf5083fe98fce1dd18540e1d0175042437a986e33eec105eca248f8d42'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/XML/Compile'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9e8ac11247f --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), + ('libxml2', '2.11.5'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 59bd0ade20f81c11e4903d57c996fb0042bae054 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 24 Oct 2024 17:22:30 +0200 Subject: [PATCH 329/524] add Perl-budle-CPAN builddep --- easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb index ad3a0522d39..63e5c0110bf 100644 --- a/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb @@ -14,6 +14,7 @@ sources = ['v%(version)s.tar.gz'] builddependencies = [ ('binutils', '2.40'), ('Rust', '1.75.0'), + ('Perl-bundle-CPAN', '5.36.1'), ] sanity_check_paths = { From 35f1475c20f8c3cd1236cfbd83e9b6973c4d3a4d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 24 Oct 2024 17:27:32 +0200 Subject: [PATCH 330/524] add Perl-budle-CPAN builddep --- easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb index 4899fba40e5..cae76ec0a45 100644 --- a/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/m/modkit/modkit-0.4.1-GCCcore-13.3.0.eb @@ -14,6 +14,7 @@ sources = ['v%(version)s.tar.gz'] builddependencies = [ ('binutils', '2.42'), ('Rust', '1.78.0'), + ('Perl-bundle-CPAN', '5.38.2'), ] sanity_check_paths = { From b86d803bc5e243d48dc48f74ea2be47a261fea8e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 24 Oct 2024 20:43:56 +0200 Subject: [PATCH 331/524] adding easyconfigs: Java-21.0.5.eb and bumping version in Java-21.eb --- easybuild/easyconfigs/j/Java/Java-21.0.5.eb | 32 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-21.eb | 2 +- 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-21.0.5.eb diff --git a/easybuild/easyconfigs/j/Java/Java-21.0.5.eb b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb new file mode 100644 index 00000000000..932318fd336 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb @@ -0,0 +1,32 @@ +name = 'Java' +version = '21.0.5' +local_build = '11' + +homepage = 'https://openjdk.org' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '3c654d98404c073b8a7e66bffb27f4ae3e7ede47d13284c132d40a83144bfd8c', + local_tarball_tmpl % ('aarch64', local_build): + '6482639ed9fd22aa2e704cc366848b1b3e1586d2bf1213869c43e80bca58fe5c', + local_tarball_tmpl % ('ppc64le', local_build): + '3c6f4c358facfb6c19d90faf02bfe0fc7512d6b0e80ac18146bbd7e0d01deeef', + local_tarball_tmpl % ('riscv64', local_build): + '2f1b3e401e36de803398dfb9818861f9f14ca8ae7db650ea0946ab048fefe3b9', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-21.eb b/easybuild/easyconfigs/j/Java/Java-21.eb index 46e84105b35..c7aef391c20 100644 --- a/easybuild/easyconfigs/j/Java/Java-21.eb +++ b/easybuild/easyconfigs/j/Java/Java-21.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.2')] +dependencies = [('Java', '%(version)s.0.5')] moduleclass = 'lang' From 02a9a7c67b71ea7ba86871ddf931f813ebc67c95 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 24 Oct 2024 21:05:28 +0200 Subject: [PATCH 332/524] Removed Szip because it's already merged --- .../s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb deleted file mode 100644 index 317db519350..00000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1.1' - -homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' - -description = """ - Szip compression software, providing lossless compression of scientific data -""" - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] - -builddependencies = [ - ('binutils', '2.42'), -] - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' From 1596a3a54a069a0d4d2e8fde41afa36787833a7a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Oct 2024 09:00:32 +0200 Subject: [PATCH 333/524] Remove jedi because it's already merged --- .../j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb deleted file mode 100644 index c4d7702a368..00000000000 --- a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jedi' -version = "0.19.1" - -homepage = 'https://github.com/davidhalter/jedi' -description = """ - Jedi - an awesome autocompletion, static analysis and refactoring library for Python. -""" - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} - -builddependencies = [ - ('binutils', '2.42'), -] -dependencies = [ - ('Python', '3.12.3'), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('parso', '0.8.4', { - 'checksums': ['eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d'], - }), - (name, version, { - 'checksums': ['cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python3.12/site-packages/jedi'], -} - -moduleclass = 'tools' From 7b13d59d8b3b402141fc36c78baf1de9231ce6c5 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 13:09:42 +0200 Subject: [PATCH 334/524] Update Shapely-2.0.6-gfbf-2024a.eb --- easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb index 6e0094044ab..4488ff1f7e4 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.12.3'), ('SciPy-bundle', '2024.05'), - ('GEOS', '3.13.0'), + ('GEOS', '3.12.2'), ] download_dep_fail = True From b16ebb2a33dbd322cbdfe625d116c6c5e533d8be Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 13:10:53 +0200 Subject: [PATCH 335/524] Delete easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb --- .../g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb deleted file mode 100644 index 11abbcb4252..00000000000 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.13.0-GCC-13.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'GEOS' -version = '3.13.0' - -homepage = 'https://trac.osgeo.org/geos' -description = "GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)" - -toolchain = {'name': 'GCC', 'version': '13.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://download.osgeo.org/geos/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['47ec83ff334d672b9e4426695f15da6e6368244214971fabf386ff8ef6df39e4'] - -builddependencies = [ - ('CMake', '3.29.3'), -] - -# Build static and shared libraries -configopts = [ - '', - '-DBUILD_SHARED_LIBS=OFF', -] - - -sanity_check_paths = { - 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], - 'dirs': [], -} - -moduleclass = 'math' From 253198299616e4069327797374e579077aa8dfa5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 25 Oct 2024 15:36:45 +0200 Subject: [PATCH 336/524] use new checksum --- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb index 7cb1689c5c2..16a08f8a296 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb index 9d094c2cb89..0d8ab51c62c 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb index 5bf659a141a..a3a016ff1ec 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb index 7cae952e521..a18a81a6e10 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb index 4ac7b2ae50d..cef52ebe349 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb index 9d2584de1bb..42efdfdbf28 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.42'), From b5f5bc0099d84dccacf39a65df24ec94b25d1455 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 25 Oct 2024 15:46:33 +0200 Subject: [PATCH 337/524] use module name in extension of SciKeras-0.12.0-foss-2022a.eb --- easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb index ef229b6885b..b25d4c4b554 100644 --- a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb @@ -22,8 +22,7 @@ use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { - 'modulename': 'scikeras', + ('scikeras', version, { 'sources': ['scikeras-%(version)s.tar.gz'], 'checksums': ['f60d81255a8904671bd33cbff060926cfa5ddd52fa234b12290afe3cb69dcc6c'], }), From c4f75f594f9bcffcedde497e71a47648b79ebef3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 25 Oct 2024 15:48:33 +0200 Subject: [PATCH 338/524] remove default sources of extension in SciKeras-0.12.0-foss-2022a.eb --- easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb index b25d4c4b554..7ef8def71d7 100644 --- a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb @@ -23,7 +23,6 @@ sanity_pip_check = True exts_list = [ ('scikeras', version, { - 'sources': ['scikeras-%(version)s.tar.gz'], 'checksums': ['f60d81255a8904671bd33cbff060926cfa5ddd52fa234b12290afe3cb69dcc6c'], }), ] From 75c10304d6d5ebfbccca7bf521e18fc6e4f549f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 25 Oct 2024 16:54:52 +0200 Subject: [PATCH 339/524] add comment about checksum change --- .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb | 2 ++ .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb | 2 ++ .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb | 2 ++ .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb | 2 ++ .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb | 2 ++ .../easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb | 2 ++ 6 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb index 16a08f8a296..a3dfd0929ae 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb index 0d8ab51c62c..0c340d04126 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb index a3a016ff1ec..d9149c29346 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb index a18a81a6e10..738875b2a89 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb index cef52ebe349..bb8e791815d 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb index 42efdfdbf28..57898c7b05c 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -31,6 +31,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ From 4af69ccb71cfe52f7038fac56a4447eba5d546e7 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 17:59:49 +0200 Subject: [PATCH 340/524] Update easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb index 5df6263ae2c..3f0dfef4b64 100644 --- a/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb @@ -29,7 +29,7 @@ configopts = "-DASSIMP_WARNINGS_AS_ERRORS=OFF " sanity_check_paths = { - 'files': ['include/%(name)s/types.h', 'lib/libassimp.so'], + 'files': ['include/%(name)s/types.h', 'lib/libassimp.%s' % SHLIB_EXT], 'dirs': [], } From c202c195e90fc8a3b367b5ac544af8c43ba77787 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 17:59:55 +0200 Subject: [PATCH 341/524] Update easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- .../double-conversion-3.3.0-GCCcore-13.3.0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb index 0b53c10d5f5..c4b5780f6ee 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb @@ -27,10 +27,9 @@ configopts = [ sanity_check_paths = { - 'files': ['include/%(name)s/bignum.h', 'include/%(name)s/cached-powers.h', 'include/%(name)s/diy-fp.h', - 'include/%(name)s/%(name)s.h', 'include/%(name)s/fast-dtoa.h', 'include/%(name)s/fixed-dtoa.h', - 'include/%(name)s/ieee.h', 'include/%(name)s/strtod.h', 'include/%(name)s/utils.h', - 'lib/libdouble-conversion.a', 'lib/libdouble-conversion.so', 'lib/libdouble-conversion_pic.a'], + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], 'dirs': [], } From 164fd0ba165d5614bc245a42d4c8249296e8af8f Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 18:00:03 +0200 Subject: [PATCH 342/524] Update easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb index dd8446f91c4..deb2902a42a 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb @@ -81,7 +81,7 @@ configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON -DBUILD_qtwayland=OFF " # configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 sanity_check_paths = { - 'files': ['bin/qmake6', 'lib/libQt6Core.so', 'lib/libQt6WebEngineCore.so'], + 'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT, 'lib/libQt6WebEngineCore.%s' % SHLIB_EXT], 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], } From 88708452008771f2998335b8eee3cd1a7b87077b Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 18:00:14 +0200 Subject: [PATCH 343/524] Update easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb index 8d1341af57b..9157abca1c4 100644 --- a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb @@ -21,9 +21,10 @@ configopts = "--disable-debug --enable-optimize --enable-64bit" sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%(version_major)s.so', - 'lib/libplc%(version_major)s.a', 'lib/libplc%(version_major)s.so', 'lib/libplds%(version_major)s.a', - 'lib/libplds%(version_major)s.so', 'lib/pkgconfig/%(namelower)s.pc'], + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/%(namelower)s.pc'], 'dirs': ['include/%(namelower)s'], } From 5beb3e722e778ff1679d2a1711f420c92b7006c1 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 25 Oct 2024 18:00:21 +0200 Subject: [PATCH 344/524] Update easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb index aaa018251cc..2310edf5555 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb @@ -31,7 +31,7 @@ configopts = [ sanity_check_paths = { - 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.so', 'include/%(name)s.h'], + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], 'dirs': [], } From dfe49901484dafe9a04fc473aae54e7ea49aa947 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 25 Oct 2024 18:20:18 +0200 Subject: [PATCH 345/524] adding easyconfigs: Trinotate-4.0.2-foss-2023a.eb, TransDecoder-5.7.1-GCC-12.3.0.eb, PyBioLib-1.1.2250-GCCcore-12.3.0.eb --- .../PyBioLib-1.1.2250-GCCcore-12.3.0.eb | 54 ++++++++++++++++++ .../TransDecoder-5.7.1-GCC-12.3.0.eb | 35 ++++++++++++ .../t/Trinotate/Trinotate-4.0.2-foss-2023a.eb | 55 +++++++++++++++++++ 3 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..02c4c54ce07 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.1.2250' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Flask', '2.3.3'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('docker', '7.1.0', { + 'checksums': ['ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c'], + }), + ('PyJWT', '2.9.0', { + 'modulename': 'jwt', + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['7e1e5b56cc735432a7369cbfa0efe50fa113ebecdc04ae6922deba8b84582d0c'], + }), + ('gunicorn', '23.0.0', { + 'checksums': ['f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'checksums': ['1a0fb4a0256bfa8345b881ac9697cf94a50bcab2caa9ad063689dfc0035fe5a2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..3f1bbc6fe83 --- /dev/null +++ b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'TransDecoder' +version = '5.7.1' + +homepage = 'https://github.com/TransDecoder/TransDecoder/wiki' +description = """TransDecoder identifies candidate coding regions within transcript sequences, + such as those generated by de novo RNA-Seq transcript assembly using Trinity, + or constructed based on RNA-Seq alignments to the genome using + Tophat and Cufflinks.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] +sources = ['TransDecoder-v%(version)s.tar.gz'] +checksums = ['41dd5e95f6ba946ff21340417d867e5e99f123b4035779b25d3cffd20b828a30'] + +dependencies = [ + ('Perl', '5.36.1'), + ('CD-HIT', '4.8.1'), +] + +sanity_check_paths = { + 'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'], + 'dirs': ['PerlLib', 'sample_data', 'util'], +} + +sanity_check_commands = [] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb new file mode 100644 index 00000000000..b5c3d27e371 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' +name = 'Trinotate' +version = '4.0.2' + +homepage = 'https://github.com/Trinotate/Trinotate/wiki' +description = """Trinotate is a comprehensive annotation suite designed for automatic functional +annotation of transcriptomes, particularly de novo assembled transcriptomes, +from model or non-model organisms. Trinotate makes use of a number of different +well referenced methods for functional annotation including homology search to +known sequence data (BLAST+/SwissProt), protein domain identification +(HMMER/PFAM), protein signal peptide and transmembrane domain prediction +(signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg +databases). All functional annotation data derived from the analysis of +transcripts is integrated into a SQLite database which allows fast efficient +searching for terms with specific qualities related to a desired scientific +hypothesis or a means to create a whole annotation report for a transcriptome.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['2f633df2e05e5d22e19159aa147060be7884a057314cad3e6db91dba8910fad1'] + +# # for reference, list of dependencies in the container image used upstream: +# # https://github.com/Trinotate/Trinotate/blob/master/Docker/Dockerfile +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('Trinity', '2.15.2'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('HMMER', '3.4'), + ('Infernal', '1.1.5'), + ('PyBioLib', '1.1.2250'), + ('SAMtools', '1.18'), + ('TransDecoder', '5.7.1'), +] + +sanity_check_paths = { + 'files': ['Trinotate', 'run_TrinotateWebserver.pl'], + 'dirs': ['PerlLib', 'resources', 'testing', 'util'], +} + +sanity_check_commands = [ + 'Trinotate --help 2>&1 | grep -q "Trinotate --db "', +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' From bacbb82000f4a14e9a20465a187f4f6163e70a1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 25 Oct 2024 20:29:01 +0200 Subject: [PATCH 346/524] adding easyconfigs: CPPE-0.3.1-GCC-12.3.0.eb --- .../c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..06b34618eb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CPPE' +version = '0.3.1' + +homepage = 'https://github.com/maxscheurer/cppe' +description = """CPPE is an open-source, light-weight C++ and Python library for Polarizable +Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE +for ground-state self-consistent field (SCF) calculations and post-SCF methods. +A convenient Python interface is also available.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'maxscheurer' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pybind11', '2.11.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('cppe', version, { + 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libcppe.%s' % SHLIB_EXT], + 'dirs': ['include/cppe', 'lib/python%(pyshortver)s/site-packages', 'share/cmake'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 7996631f92066680d5e77b27e085b7ba1c9c7d30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 25 Oct 2024 20:33:02 +0200 Subject: [PATCH 347/524] lower the `CPPE` dependency version --- easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb index 72432ce1b97..d2efdfa6e27 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb @@ -23,7 +23,7 @@ dependencies = [ ('libcint', '5.4.0'), ('libxc', '6.2.2'), ('XCFun', '2.1.1'), - ('CPPE', '0.3.3a0'), # extra + ('CPPE', '0.3.1'), # extra ('PyBerny', '0.6.3'), # extra ('PyCheMPS2', '1.8.12'), # needed by dmrgscf ('Block', '1.5.3-20200525'), # needed by dmrgscf From c2c9d2aec78966c55b91776334d5f76915093502 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 28 Oct 2024 10:34:57 +0100 Subject: [PATCH 348/524] pydot as dependency instead of extension --- easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb index 0717fc8e997..9b14f9ce1be 100644 --- a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb @@ -21,15 +21,13 @@ dependencies = [ ('pymatgen', '2023.3.10'), # for pybtex and latexcodec ('matplotlib', '3.5.2'), ('pygraphviz', '1.10'), + ('pydot', '1.4.2'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('pydot', '2.0.0', { - 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], - }), (name, version, { 'modulename': 'sciann', 'checksums': ['7d7acf61346b4201628c5656e2c904e9a9c7cda78086e76d075b5c7bb90adf3c'], From 6b8b53493a1188a5baa56a133574daac239730e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 28 Oct 2024 10:57:07 +0100 Subject: [PATCH 349/524] remove -m64 flag for architectures other than x86-64 --- .../s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb | 4 ++++ .../s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb | 4 ++++ .../s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb | 4 ++++ .../s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb | 4 ++++ .../s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb | 4 ++++ .../s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb | 4 ++++ 6 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb index a3dfd0929ae..30b9729414a 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.37'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb index 0c340d04126..f948c852c2d 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.38'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb index d9149c29346..3921083e94f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.39'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb index 738875b2a89..2a1c723de5a 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.40'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb index bb8e791815d..90f04ab5dff 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.40'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb index 57898c7b05c..ff0762c0c4e 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -39,6 +39,10 @@ builddependencies = [ ('binutils', '2.42'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: From 86bc145a09cbd7ccc3d0ba96dda3b533a9dabe12 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Mon, 28 Oct 2024 17:01:54 +0100 Subject: [PATCH 350/524] Add Intel 2025.0.0 compilers MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../intel-compilers-2025.0.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb new file mode 100644 index 00000000000..34a1074639e --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/ac92f2bb-4818-4e53-a432-f8b34d502f23/' + ], + 'filename': 'intel-dpcpp-cpp-compiler-%(version)s.740_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/69f79888-2d6c-4b20-999e-e99d72af68d4/' + ], + 'filename': 'intel-fortran-compiler-%(version)s.723_offline.sh', + }, +] +checksums = [ + {'intel-dpcpp-cpp-compiler-2025.0.0.740_offline.sh': + '04fadf63789acee731895e631db63f65a98b8279db3d0f48bdf0d81e6103bdd8'}, + {'intel-fortran-compiler-2025.0.0.723_offline.sh': + '2be6d607ce84f35921228595b118fbc516d28587cbc4e6dcf6b7219e5cd1a9a9'}, +] + +local_gccver = '14.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' From c796315c43a2a30ee2a06af4059d3553a044a342 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:46:57 +0100 Subject: [PATCH 351/524] adding easyconfigs: tbl2asn-20230713-GCCcore-12.3.0.eb --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1e03c1f4e24 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' + +# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " +# " echo setting RPATH in $lib;" +# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" +# " done;" +# +# + +""" + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" + "fi", +""" \ No newline at end of file From 206e1526e91256577afbf6a661b8e2e9dfee3f69 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:50:53 +0100 Subject: [PATCH 352/524] clean up config --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 26 +------------------ 1 file changed, 1 insertion(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 1e03c1f4e24..68563984e25 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,28 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' - -# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " -# " echo setting RPATH in $lib;" -# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" -# " done;" -# -# - -""" - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" - "fi", -""" \ No newline at end of file +moduleclass = 'bio' \ No newline at end of file From 5af534809483cf5d2b0d70beb583375d0ca4bc3c Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 28 Oct 2024 18:12:14 +0100 Subject: [PATCH 353/524] adding easyconfigs: PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb --- .../PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..274fd6d6c42 --- /dev/null +++ b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'JAR' + +name = 'PoPoolation-TE2' +version = '1.10.03' + +homepage = 'https://sourceforge.net/p/popoolation-te2/wiki/Home/' +description = """ +PoPoolationTE2: enables comparative population genomics of transposable elements (TE). As a +major innovation PoPoolation TE2 introduces the physical pileup file which allows to +homogenize the power to identify TEs and thus enables an unbiased comparison of TE abundance +between samples, where samples could be pooled populations, tissues or sequenced individuals. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('BWA', '0.7.17'), + ('Java', '17', '', SYSTEM), +] + +source_urls = ['https://sourceforge.net/projects/popoolation-te2/files/'] +sources = [ + { + 'filename': 'popte2.jar', + 'download_filename': 'popte2-v%(version)s.jar', + }, + 'walkthrough-refgenome.zip', + 'walkthrough-reads.zip', + +] +checksums = [ + {'popte2.jar': '95eca422a6d295277d20ec1cbbcb9000bad1f380ae7cba9005f20ff211907e32'}, + {'walkthrough-refgenome.zip': 'ce3cb0b952a99fcae6b348cd888ee6f4c3a45d7e0b208e211ecb290cacde618c'}, + {'walkthrough-reads.zip': '909a8f1d507bb20518f6ef1ac313a59b8e8b02b70fc911e2d6d6efdce2e258f3'}, +] + +postinstallcmds = [ + "cd %(installdir)s && unzip walkthrough-refgenome.zip", + "cd %(installdir)s && unzip walkthrough-reads.zip", + "cd %(installdir)s && rm walkthrough-refgenome.zip walkthrough-reads.zip", +] + +sanity_check_commands = [ + 'java -jar $EBROOTPOPOOLATIONMINTE2/popte2.jar --help 2>&1 | grep "Usage: java"', +] + +sanity_check_paths = { + 'files': ['popte2.jar'], + 'dirs': ['walkthrough-refgenome', 'walkthrough-reads'], +} + +modloadmsg = """ +To execute PoPoolation-TE2 run: java -jar $EBROOTPOPOOLATIONMINTE2/popte2.jar +The reference genome and the Te-hierachy can be found in $EBROOTPOPOOLATIONMINTE2/walkthrough-refgenome +Reads provided by the developer can be found under $EBROOTPOPOOLATIONMINTE2/walkthrough-reads +""" + +moduleclass = 'bio' From 8bf310cc1a2901cebd5ddfd308dfc3626c375929 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 18:19:49 +0100 Subject: [PATCH 354/524] add blank line to end of file --- .../easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 68563984e25..dcf4c39e8d0 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,4 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 45228482140e7ae954605dcd6432f33994126514 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 18:48:14 +0100 Subject: [PATCH 355/524] change tbl2asn version that is compatible with RPATH enabled builds see #21756 --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index 0eeac174f28..ed9d5580415 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -18,7 +18,7 @@ dependencies = [ ('matplotlib', '3.7.2'), ('scikit-learn', '1.3.1'), ('Seaborn', '0.13.2'), - ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('tbl2asn', '20230713'), ('DBD-mysql', '4.050'), ('CodingQuarry', '2.0'), ('Trinity', '2.15.2'), From cb49d8c1f417ff6e4c5f736916a76751f72ce290 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 28 Oct 2024 23:57:53 +0100 Subject: [PATCH 356/524] Add bot for tagging new and updated ECs --- .github/workflows/tagbot.py | 169 +++++++++++++++++++++++++++++++++++ .github/workflows/tagbot.yml | 25 ++++++ 2 files changed, 194 insertions(+) create mode 100644 .github/workflows/tagbot.py create mode 100644 .github/workflows/tagbot.yml diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py new file mode 100644 index 00000000000..0583e9ee0e7 --- /dev/null +++ b/.github/workflows/tagbot.py @@ -0,0 +1,169 @@ +import os +import git +import requests +import json +import difflib +from datetime import datetime +from pathlib import Path + + +def get_first_commit_date(repo, file_path): + print(f"Checking commit dates for {file_path}") + commits = list(repo.iter_commits(paths=file_path)) + if commits: + return commits[-1].committed_date + else: + print(f"{file_path} has no commit info, putting it last") + return datetime.datetime.min + + +def sort_by_added_date(repo, file_paths): + print("Compute first commit dates") + files_with_dates = [(get_first_commit_date(repo, file_path), file_path) for file_path in file_paths] + sorted_files = sorted(files_with_dates, reverse=True) + return [file for date, file in sorted_files] + + +def similar_easyconfigs(repo, new_file): + possible_neighbours = [x for x in new_file.parent.glob('*.eb') if x != new_file] + return sort_by_added_date(repo, possible_neighbours)[:3] # top 3 choices + + +def diff(old, new): + print(f"Diffing {old} vs {new}") + with open(old, 'r') as old_file, open(new, 'r') as new_file: + old_lines = list(old_file) + new_lines = list(new_file) + return ''.join(difflib.unified_diff( + old_lines, + new_lines, + fromfile=str(old), + tofile=str(new))) + + +def pr_ecs(pr_diff): + news_ecs = [] + changed_ecs = [] + for item in pr_diff: + if item.a_path.endswith('.eb'): + if item.change_type == 'A': + new_ecs.append(Path(item.a_path)) + else: + changed_ecs.append(Path(item.a_path)) + return new_ecs, changed_ecs + + +GITHUB_API_URL = 'https://api.github.com' +event_path = os.getenv("GITHUB_EVENT_PATH") +token = os.getenv("GH_TOKEN") +repo = os.getenv("GITHUB_REPOSITORY") +base_branch_name = os.getenv("GITHUB_BASE_REF") +pr_branch_name = os.getenv("GITHUB_HEAD_REF") + +with open(event_path) as f: + data = json.load(f) + +pr_number = data['pull_request']['number'] + +print("PR number:", pr_number) +print("Repo:", repo) +print("Base branch name:", base_branch_name) +print("PR branch name:", pr_branch_name) + +gitrepo = git.Repo(".") +branches = {x.name: x for x in gitrepo.remote().refs} +base_branch = branches['origin/' + base_branch_name] +pr_branch = branches['origin/' + pr_branch_name] + +pr_diff = base_branch.commit.diff(pr_branch.commit) +new_ecs, changed_ecs = pr_ecs(pr_diff) + +print("Changed ECs:", changed_ecs) +print("Newly added ECs:", new_ecs) + +new_software = False +updated_software = False +comment = '' +for new_file in new_ecs: + neighbours = similar_easyconfigs(gitrepo, new_file) + print(f"Found {len(neighbours)} neighbours for {new_file}") + if neighbours: + updated_software = True + print(f"Diffs for {new_file}") + comment += f'#### Updated software `{new_file.name}`\n\n' + + for neighbour in neighbours: + print(f"against {neighbour}") + comment += '
\n' + comment += f'Diff against {neighbour.name}\n\n' + comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' + comment += '```diff\n' + comment += diff(neighbour, new_file) + comment += '```\n
\n' + else: + new_software = True + + +print("Adjusting labels") +current_labels = [label['name'] for label in data['pull_request']['labels']] + +labels_add = [] +labels_del = [] +for condition, label in [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]: + if condition and label not in current_labels: + labels_add.append(label) + elif not condition and label in current_labels: + labels_del.append(label) + +url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/labels" + +headers = { + "Accept": "application/vnd.github+json", + "Authorization": f"Bearer {token}", + "X-GitHub-Api-Version": f"2022-11-28", +} + +if labels_add: + print(f"Setting labels: {labels_add} at {url}") + response = requests.post(url, headers=headers, json={"labels": labels_add}) + if response.status_code == 200: + print(f"Labels {labels_add} added successfully.") + else: + print(f"Failed to add labels: {response.status_code}, {response.text}") + +for label in labels_del: + print(f"Removing label: {label} at {url}") + response = requests.delete(f'{url}/{label}', headers=headers) + if response.status_code == 200: + print(f"Label {label} removed successfully.") + else: + print(f"Failed to delete label: {response.status_code}, {response.text}") + +# Write comment with diff +if updated_software: + # Search for comment by bot to potentially replace + url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/comments" + response = requests.get(url, headers=headers) + comment_id = None + for existing_comment in response.json(): + if existing_comment["user"]["login"] == "github-actions[bot]": # Bot username in GitHub Actions + comment_id = existing_comment["id"] + + if comment_id: + # Update existing comment + url = f"{GITHUB_API_URL}/repos/{repo}/issues/comments/{comment_id}" + response = requests.patch(url, headers=headers, json={"body": comment}) + if response.status_code == 200: + print("Comment updated successfully.") + else: + print(f"Failed to update comment: {response.status_code}, {response.text}") + else: + # Post a new comment + url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/comments" + response = requests.post(url, headers=headers, json={"body": comment}) + if response.status_code == 201: + print("Comment posted successfully.") + else: + print(f"Failed to post comment: {response.status_code}, {response.text}") + + diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml new file mode 100644 index 00000000000..1c45d57cd76 --- /dev/null +++ b/.github/workflows/tagbot.yml @@ -0,0 +1,25 @@ +name: Tagbot +on: [pull_request] + +permissions: + pull-requests: write + +jobs: + tagbot: + runs-on: ubuntu-20.04 + steps: + - uses: actions/checkout@v4 + + - name: set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.12 + + - name: Get packages + run: pip install gitpython requests + + - name: Tag and comment + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: python .github/workflows/tagbot.py + From 7eb56cc5b50779e02c66039991d9a165b8cdb4af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Oct 2024 00:20:52 +0100 Subject: [PATCH 357/524] Add a new easyconfig as an example. --- .../n/networkx/networkx-3.4.2-gfbf-2024a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb new file mode 100644 index 00000000000..9adfd4d5246 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.4.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From a5b95e8875fcae4022771fd4aebd48c9d0f777ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Oct 2024 00:28:57 +0100 Subject: [PATCH 358/524] Fix style errors in tagbot --- .github/workflows/tagbot.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 0583e9ee0e7..5134dbae6ef 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -26,7 +26,7 @@ def sort_by_added_date(repo, file_paths): def similar_easyconfigs(repo, new_file): possible_neighbours = [x for x in new_file.parent.glob('*.eb') if x != new_file] - return sort_by_added_date(repo, possible_neighbours)[:3] # top 3 choices + return sort_by_added_date(repo, possible_neighbours)[:3] # top 3 choices def diff(old, new): @@ -39,10 +39,10 @@ def diff(old, new): new_lines, fromfile=str(old), tofile=str(new))) - + def pr_ecs(pr_diff): - news_ecs = [] + new_ecs = [] changed_ecs = [] for item in pr_diff: if item.a_path.endswith('.eb'): @@ -111,16 +111,16 @@ def pr_ecs(pr_diff): labels_del = [] for condition, label in [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]: if condition and label not in current_labels: - labels_add.append(label) + labels_add.append(label) elif not condition and label in current_labels: - labels_del.append(label) + labels_del.append(label) url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/labels" headers = { "Accept": "application/vnd.github+json", "Authorization": f"Bearer {token}", - "X-GitHub-Api-Version": f"2022-11-28", + "X-GitHub-Api-Version": "2022-11-28", } if labels_add: @@ -165,5 +165,3 @@ def pr_ecs(pr_diff): print("Comment posted successfully.") else: print(f"Failed to post comment: {response.status_code}, {response.text}") - - From bbaf8bdeda34c154da332b67e8791d755892c4a8 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Tue, 29 Oct 2024 09:40:36 +0100 Subject: [PATCH 359/524] Set JAVA version to variant of toolchain --- .../p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb index 274fd6d6c42..e93f4a079c6 100644 --- a/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [('binutils', '2.40')] dependencies = [ ('BWA', '0.7.17'), - ('Java', '17', '', SYSTEM), + ('Java', '11', '', SYSTEM), ] source_urls = ['https://sourceforge.net/projects/popoolation-te2/files/'] From 79caf6eec4c38c9507f4c05db9786e71558f91c1 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 29 Oct 2024 12:21:51 +0000 Subject: [PATCH 360/524] Build PyCUDA with OpenGL support --- .../p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb index 0058b158c9e..1706b5b8372 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb @@ -14,6 +14,7 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('Mako', '1.2.4'), + ('PyOpenGL', '3.1.7'), ] use_pip = True @@ -23,12 +24,15 @@ exts_list = [ 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], }), (name, version, { - 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" && ', + 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" --cuda-enable-gl && ', 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['d50d23ff6371482cff7d4b953ef40ab81c9df038ecb614484f9fd5347327327e'], }), ] sanity_pip_check = True +sanity_check_commands = [ + 'python -c "import pycuda.gl"' +] moduleclass = 'lang' From 12736996e8350448bd368e6e8de0f7c5d21eb238 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Oct 2024 22:58:34 +0100 Subject: [PATCH 361/524] Rework git refs --- .github/workflows/tagbot.py | 13 +++++++------ .github/workflows/tagbot.yml | 2 ++ 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 5134dbae6ef..3598b6bc0a9 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -58,7 +58,7 @@ def pr_ecs(pr_diff): token = os.getenv("GH_TOKEN") repo = os.getenv("GITHUB_REPOSITORY") base_branch_name = os.getenv("GITHUB_BASE_REF") -pr_branch_name = os.getenv("GITHUB_HEAD_REF") +pr_ref_name = os.getenv("GITHUB_REF_NAME") with open(event_path) as f: data = json.load(f) @@ -68,14 +68,15 @@ def pr_ecs(pr_diff): print("PR number:", pr_number) print("Repo:", repo) print("Base branch name:", base_branch_name) -print("PR branch name:", pr_branch_name) +print("PR ref:", pr_ref_name) gitrepo = git.Repo(".") -branches = {x.name: x for x in gitrepo.remote().refs} -base_branch = branches['origin/' + base_branch_name] -pr_branch = branches['origin/' + pr_branch_name] -pr_diff = base_branch.commit.diff(pr_branch.commit) + +target_commit = gitrepo.commit('origin/' + base_branch_name) +pr_commit = gitrepo.commit('pull/' + pr_ref_name) +pr_diff = target_commit.diff(pr_commit) + new_ecs, changed_ecs = pr_ecs(pr_diff) print("Changed ECs:", changed_ecs) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 1c45d57cd76..68c8247c687 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -9,6 +9,8 @@ jobs: runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v4 + with: + fetch-depth: 0 - name: set up Python uses: actions/setup-python@v5 From 878828c69367f0a7274765553b9645ff228f3780 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Oct 2024 23:19:17 +0100 Subject: [PATCH 362/524] Tone down debug verboseness --- .github/workflows/tagbot.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 3598b6bc0a9..79c698306ab 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -8,7 +8,6 @@ def get_first_commit_date(repo, file_path): - print(f"Checking commit dates for {file_path}") commits = list(repo.iter_commits(paths=file_path)) if commits: return commits[-1].committed_date @@ -18,7 +17,6 @@ def get_first_commit_date(repo, file_path): def sort_by_added_date(repo, file_paths): - print("Compute first commit dates") files_with_dates = [(get_first_commit_date(repo, file_path), file_path) for file_path in file_paths] sorted_files = sorted(files_with_dates, reverse=True) return [file for date, file in sorted_files] @@ -30,7 +28,6 @@ def similar_easyconfigs(repo, new_file): def diff(old, new): - print(f"Diffing {old} vs {new}") with open(old, 'r') as old_file, open(new, 'r') as new_file: old_lines = list(old_file) new_lines = list(new_file) From de85cbb84e1f70c3cde0a627f217f74392935e26 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 30 Oct 2024 10:50:00 +0100 Subject: [PATCH 363/524] OpenBLAS sequential with 64 bit interface --- .../OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb new file mode 100644 index 00000000000..8b0c54b4248 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb @@ -0,0 +1,55 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.11.5'), +] + +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +installopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 5a34a059effa7c989a9c73b251f1d3ff45f4db07 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 30 Oct 2024 10:56:30 +0100 Subject: [PATCH 364/524] adding easyconfigs: MrBayes-3.2.7-gompi-2023a.eb --- .../m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb new file mode 100644 index 00000000000..a3537244720 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.2'), + ('beagle-lib', '4.0.1', '-CUDA-12.1.1'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'], +} + +sanity_check_commands = ['mb -h'] + +moduleclass = 'bio' From 59142601bafbc8001aadce45f6813f4359b7b444 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 30 Oct 2024 11:27:01 +0100 Subject: [PATCH 365/524] include DB as it is no longer a dependency of Perl or Perl-bundle-CPAN --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 8ecc76c588a..867969666e1 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -40,6 +40,7 @@ dependencies = [ ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), ('Perl-bundle-CPAN', '5.36.1'), + ('DB', '18.1.40'), # for DB_File ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('BLAST+', '2.14.1'), From 85cb7520689f4da69fd77dc5149f6bd178bf69d6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 30 Oct 2024 11:52:03 +0100 Subject: [PATCH 366/524] remove setuptools-scm extension --- .../easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb index 9ff4d7c1b9c..fd593a4bb09 100644 --- a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -25,11 +25,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('setuptools-scm', '8.1.0', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], - 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], - }), # sparse needs setuptools-scm>=8 ('sparse', '0.15.4', { + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", 'checksums': ['d4b1c57d24ff0f64f2fd5b5a95b49b7fb84ed207a26d7d58ce2764dcc5c72b84'], }), ('dask-glm', '0.3.2', { From 2f16e34b3ecaa491f50127ce4382db1969e6ca88 Mon Sep 17 00:00:00 2001 From: pecar Date: Wed, 30 Oct 2024 13:38:30 +0100 Subject: [PATCH 367/524] adding easyconfigs: BCFtools-1.21-GCC-13.3.0.eb, GSL-2.8-GCC-13.3.0.eb, HTSlib-1.21-GCC-13.3.0.eb, SAMtools-1.21-GCC-13.3.0.eb --- .../b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb | 40 ++++++++++++++++++ .../easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb | 25 +++++++++++ .../h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb | 41 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb | 38 +++++++++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..ad508758ba5 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +# Updated to 1.21 jpecar / EMBL + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] + +dependencies = [ + ('zlib', '1.3.1'), + ('HTSlib', '1.21'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('GSL', '2.8'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'], + 'dirs': ['libexec/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..251304ed936 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.8' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..2f35f9fa5a2 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT +# Updated to 1.21 jpecar EMBL + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..775ce37b311 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,38 @@ +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT +# Updated to 1.21 jpecar / EMBL + +name = 'SAMtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['05724b083a6b6f0305fcae5243a056cc36cf826309c3cb9347a6b89ee3fc5ada'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +moduleclass = 'bio' From f747dc2ffc473057659983667dd2596b262ec52a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 30 Oct 2024 13:49:57 +0100 Subject: [PATCH 368/524] adding easyconfigs: OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb, Statistics-R-0.34-foss-2023a.eb --- ...0.9.0-20240703-foss-2023a-Python-3.11.3.eb | 64 +++++++++++++++++++ .../Statistics-R-0.34-foss-2023a.eb | 28 ++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb create mode 100644 easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb new file mode 100644 index 00000000000..0c101c27d2f --- /dev/null +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb @@ -0,0 +1,64 @@ +easyblock = 'MakeCp' + +name = 'OPERA-MS' +local_commit = '026f9a5' +version = '0.9.0-20240703' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/CSB5/OPERA-MS' +description = """OPERA-MS is a hybrid metagenomic assembler which combines the + advantages of short and long-read technologies to provide high quality + assemblies, addressing issues of low contiguity for short-read only assemblies, + and low base-pair quality for long-read only assemblies.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['72a3e16287dd1f2098adac41930d6a54779a033f5bf78c2659580afae5a7280c'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Statistics-R', '0.34'), + ('Python', '3.11.3'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + 'OPERA-MS.pl', + 'bin', + 'src_utils', + 'tools_opera_ms', + (['OPERA-LG/bin'], 'OPERA-LG'), +] + +postinstallcmds = [ + "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", + 'chmod +x %(installdir)s/bin/OPERA-MS', + 'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl', + '%(installdir)s/bin/OPERA-MS ' + ' '.join([ + '--contig-file test_files/contigs.fasta', + '--short-read1 test_files/R1.fastq.gz', + '--short-read2 test_files/R2.fastq.gz', + '--long-read test_files/long_read.fastq', + '--no-ref-clustering', + '--out-dir $TMPDIR', + ]), +] + +fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl'] +fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/OPERA-MS'], + 'dirs': [], +} + +sanity_check_commands = [ + 'OPERA-MS --help', + 'OPERA-MS check-dependency', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb new file mode 100644 index 00000000000..7a351d75a26 --- /dev/null +++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Statistics-R' +version = '0.34' + +homepage = 'https://metacpan.org/pod/Statistics::R' +description = "Perl interface with the R statistical program" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY'] +sources = [SOURCE_TAR_GZ] +checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), +] + +options = {'modulename': 'Statistics::R'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'], +} + +moduleclass = 'data' From 75a3c1fbd3b63511c4f595d30e0e9303c7dad103 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 30 Oct 2024 14:24:49 +0100 Subject: [PATCH 369/524] Update OPERA-MS-0.9.0 - remove versionsuffix --- .../OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb index 0c101c27d2f..8965539613c 100644 --- a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb @@ -3,7 +3,6 @@ easyblock = 'MakeCp' name = 'OPERA-MS' local_commit = '026f9a5' version = '0.9.0-20240703' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/CSB5/OPERA-MS' description = """OPERA-MS is a hybrid metagenomic assembler which combines the From 3ddbdd7a6184d643cb04aeb2ce3faf2ceeab0e81 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 30 Oct 2024 16:21:54 +0100 Subject: [PATCH 370/524] fix name of opera file --- ...23a-Python-3.11.3.eb => OPERA-MS-0.9.0-20240703-foss-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/OPERA-MS/{OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb => OPERA-MS-0.9.0-20240703-foss-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb similarity index 100% rename from easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb rename to easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb From 126524215669128d5168d53a6d050d5eccbe29e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Oct 2024 18:31:13 +0100 Subject: [PATCH 371/524] Protect workflow against modifications. Missing newline before headers --- .github/workflows/tagbot.py | 4 ++-- .github/workflows/tagbot.yml | 9 ++++++--- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 79c698306ab..8a44c8ad38b 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -83,7 +83,7 @@ def pr_ecs(pr_diff): updated_software = False comment = '' for new_file in new_ecs: - neighbours = similar_easyconfigs(gitrepo, new_file) + neighbours = similar_easyconfigs(gitrepo, new_file, new_ecs) print(f"Found {len(neighbours)} neighbours for {new_file}") if neighbours: updated_software = True @@ -97,7 +97,7 @@ def pr_ecs(pr_diff): comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' comment += '```diff\n' comment += diff(neighbour, new_file) - comment += '```\n\n' + comment += '```\n\n\n' else: new_software = True diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 68c8247c687..cea22e430e9 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -1,17 +1,20 @@ name: Tagbot on: [pull_request] -permissions: - pull-requests: write - jobs: tagbot: runs-on: ubuntu-20.04 + permissions: + pull-requests: write steps: - uses: actions/checkout@v4 with: fetch-depth: 0 + - run: | + # Make sure the script is unmodified + echo "01ddabda0825925dea0f8aa9b84b58b3d2973bb4837651d0ecf0ebe62904f67b .github/workflows/tagbot.py"|sha256sum --check --status + - name: set up Python uses: actions/setup-python@v5 with: From b74b980f07f7b01e6549b68220bd2b4d4c933c1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Oct 2024 18:35:30 +0100 Subject: [PATCH 372/524] Fix typo --- .github/workflows/tagbot.py | 2 +- .github/workflows/tagbot.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 8a44c8ad38b..b361ba3641c 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -83,7 +83,7 @@ def pr_ecs(pr_diff): updated_software = False comment = '' for new_file in new_ecs: - neighbours = similar_easyconfigs(gitrepo, new_file, new_ecs) + neighbours = similar_easyconfigs(gitrepo, new_file) print(f"Found {len(neighbours)} neighbours for {new_file}") if neighbours: updated_software = True diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index cea22e430e9..f9ec29a0f08 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -13,7 +13,7 @@ jobs: - run: | # Make sure the script is unmodified - echo "01ddabda0825925dea0f8aa9b84b58b3d2973bb4837651d0ecf0ebe62904f67b .github/workflows/tagbot.py"|sha256sum --check --status + echo "9763efd8ceb7b8fb85573e8180e8b0dcac1a4d53d5b7a69fbbf0ac8d4584ccd9 .github/workflows/tagbot.py"|sha256sum --check --status - name: set up Python uses: actions/setup-python@v5 From e0feb27e56f169513967e47a692e5de22b38b409 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 31 Oct 2024 11:40:29 +0100 Subject: [PATCH 373/524] Update BEDTools-2.31.1-GCC-13.3.0.eb --- .../easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb index 6bcbf918ae0..8503277b570 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb @@ -44,8 +44,8 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'bin/pairToBed', 'bin/mergeBed', 'bin/bedToBam', 'bin/fastaFromBed'], - 'dirs': ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, } sanity_check_commands = ['%(namelower)s --help'] From c3b3f1def78b489f45b60f55ad3f439c56285ca4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 31 Oct 2024 13:42:42 +0100 Subject: [PATCH 374/524] fix parameter redefinition --- easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb index a9853cde523..77e022aa0cf 100644 --- a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -10,7 +10,6 @@ description = """TBLIS is a library and framework for performing tensor toolchain = {'name': 'foss', 'version': '2023a'} -sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/devinamatthews/tblis/archive/'] sources = ['%s.tar.gz' % local_commit] checksums = ['85b72884022edd2612e3a0b3ed12aa6237d3989b581091d21f58124a7450aaeb'] From 15c7a2db6bc7000727b532342478ea044f713403 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 31 Oct 2024 13:50:35 +0100 Subject: [PATCH 375/524] Drop example update easyconfig from PR --- .../n/networkx/networkx-3.4.2-gfbf-2024a.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb deleted file mode 100644 index 9adfd4d5246..00000000000 --- a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '3.4.2' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, -and study of the structure, dynamics, and functions of complex networks.""" - -toolchain = {'name': 'gfbf', 'version': '2024a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1'] - -dependencies = [ - ('Python', '3.12.3'), - ('SciPy-bundle', '2024.05'), # required for numpy, scipy, ... -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'tools' From 6a4e1fe808ac0989454d2bc48fbb710a4edd9dd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 31 Oct 2024 13:51:32 +0100 Subject: [PATCH 376/524] Update workflow OS to ubuntu 24.04 --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index f9ec29a0f08..f7cd539226f 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -3,7 +3,7 @@ on: [pull_request] jobs: tagbot: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 permissions: pull-requests: write steps: From c3a316441e8a972e870443e6079d712ed96add0d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 31 Oct 2024 13:54:48 +0100 Subject: [PATCH 377/524] fix ncurses problem --- .../o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb index 8965539613c..620366c965b 100644 --- a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb @@ -21,8 +21,12 @@ dependencies = [ ('Perl-bundle-CPAN', '5.36.1'), ('Statistics-R', '0.34'), ('Python', '3.11.3'), + ('SAMtools', '0.1.20'), ] +prebuildopts = 'rm %(start_dir)s/tools_opera_ms/samtools && ' +prebuildopts += 'cd %(start_dir)s/tools_opera_ms && ln -s $EBROOTSAMTOOLS/bin/samtools && ' +prebuildopts += 'cd %(start_dir)s &&' buildopts = 'CFLAGS="$CFLAGS"' files_to_copy = [ From 8d34813396a03266b758ae8cccf467308ae3fe31 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 31 Oct 2024 14:58:50 +0100 Subject: [PATCH 378/524] Update easyconfigs.py - add exception for OPERA-MS and SAMtools --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index eca5c4e2add..8279a98c16b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -629,7 +629,7 @@ def check_dep_vars(self, gen, dep, dep_vars): ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', - r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1', r'OPERA-MS-0\.9\.0-20240703'])], # NanoPlot, NanoComp use an older version of Seaborn 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], # Shasta requires spoa 3.x From f469159872324254494c581b6e61544b4c39e811 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 31 Oct 2024 16:23:50 +0100 Subject: [PATCH 379/524] Limit number of diffs for large PRs --- .github/workflows/tagbot.py | 39 ++++++++++++++++++++++++++---------- .github/workflows/tagbot.yml | 2 +- 2 files changed, 29 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index b361ba3641c..9c9710e9a46 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -24,7 +24,7 @@ def sort_by_added_date(repo, file_paths): def similar_easyconfigs(repo, new_file): possible_neighbours = [x for x in new_file.parent.glob('*.eb') if x != new_file] - return sort_by_added_date(repo, possible_neighbours)[:3] # top 3 choices + return sort_by_added_date(repo, possible_neighbours) def diff(old, new): @@ -79,18 +79,38 @@ def pr_ecs(pr_diff): print("Changed ECs:", changed_ecs) print("Newly added ECs:", new_ecs) -new_software = False -updated_software = False -comment = '' +new_software = 0 +updated_software = 0 +to_diff = dict() for new_file in new_ecs: neighbours = similar_easyconfigs(gitrepo, new_file) print(f"Found {len(neighbours)} neighbours for {new_file}") if neighbours: - updated_software = True - print(f"Diffs for {new_file}") - comment += f'#### Updated software `{new_file.name}`\n\n' + updated_software += 1 + to_diff[new_file] = neighbours + else: + new_software += 1 + +print(f"Generating comment for {len(to_diff)} updates softwares") +# Limit comment size for large PRs: +if len(to_diff) > 20: # Too much, either bad PR or some broad change. Not diffing. + max_diffs_per_software = 0 +elif len(to_diff) > 10: + max_diffs_per_software = 1 +elif len(to_diff) > 5: + max_diffs_per_software = 2 +else: + max_diffs_per_software = 3 - for neighbour in neighbours: +comment = '' +if max_diffs_per_software > 0: + for new_file, neighbours in to_diff.items(): + compare_neighbours = neighbours[:max_diffs_per_software] + if compare_neighbours: + print(f"Diffs for {new_file}") + comment += f'#### Updated software `{new_file.name}`\n\n' + + for neighbour in compare_neighbours: print(f"against {neighbour}") comment += '
\n' comment += f'Diff against {neighbour.name}\n\n' @@ -98,9 +118,6 @@ def pr_ecs(pr_diff): comment += '```diff\n' comment += diff(neighbour, new_file) comment += '```\n
\n\n' - else: - new_software = True - print("Adjusting labels") current_labels = [label['name'] for label in data['pull_request']['labels']] diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index f7cd539226f..1d382dae51d 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -13,7 +13,7 @@ jobs: - run: | # Make sure the script is unmodified - echo "9763efd8ceb7b8fb85573e8180e8b0dcac1a4d53d5b7a69fbbf0ac8d4584ccd9 .github/workflows/tagbot.py"|sha256sum --check --status + echo "8be2d295e8436ce557acc8a4d3b82a639913ae65de0d1a76871f21359b4e8d9f .github/workflows/tagbot.py"|sha256sum --check --status - name: set up Python uses: actions/setup-python@v5 From ef7b6125cb558856f8905c85309451acc0415846 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 31 Oct 2024 18:30:19 +0100 Subject: [PATCH 380/524] add missing perl-bundle-cpan to recent parallel versions --- .../p/parallel/parallel-20230722-GCCcore-12.3.0.eb | 10 ++++++++-- .../p/parallel/parallel-20240322-GCCcore-13.2.0.eb | 10 ++++++++-- .../p/parallel/parallel-20240722-GCCcore-13.3.0.eb | 10 ++++++++-- 3 files changed, 24 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb index 7725cf4990a..32a4662d685 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb @@ -14,13 +14,19 @@ checksums = ['55f991ad195a72f0abfaf1ede8fc1d03dd255cac91bc5eb900f9aa2873d1ff87'] builddependencies = [('binutils', '2.40')] -dependencies = [('Perl', '5.36.1')] +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] } -sanity_check_commands = ["parallel --help"] +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb index 53acb414c76..4673651a654 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb @@ -14,13 +14,19 @@ checksums = ['0b17029a203dabf7ba6ca7e52c2d3910fff46b2979476e12a9110920b79e6a95'] builddependencies = [('binutils', '2.40')] -dependencies = [('Perl', '5.38.0')] +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), +] sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] } -sanity_check_commands = ["parallel --help"] +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb index 92658cc24b7..e3f60b06f2c 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb @@ -14,13 +14,19 @@ checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0'] builddependencies = [('binutils', '2.42')] -dependencies = [('Perl', '5.38.2')] +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), +] sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] } -sanity_check_commands = ["parallel --help"] +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] moduleclass = 'tools' From 9bcf061ae395e47018b751a8cc16bf8a7c0bd0a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 09:48:59 +0000 Subject: [PATCH 381/524] adding easyconfigs: networkx-3.4.2-gfbf-2024a.eb --- .../n/networkx/networkx-3.4.2-gfbf-2024a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb new file mode 100644 index 00000000000..9adfd4d5246 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.4.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 2865dbcf398ea2f0e8cda181f7048bfa84696d52 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 11:21:20 +0100 Subject: [PATCH 382/524] Change tagbot workflow to run on pull_request_target --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 1d382dae51d..2b8c4e3ce1c 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -1,5 +1,5 @@ name: Tagbot -on: [pull_request] +on: [pull_request_target] jobs: tagbot: From d2f33da9d7ddbdf1bb6396c906bd4a50a5a1a945 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 11:28:50 +0100 Subject: [PATCH 383/524] Add comments describing permissions on tagbot --- .github/workflows/tagbot.py | 4 ++++ .github/workflows/tagbot.yml | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 9c9710e9a46..649dd1dd828 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -1,3 +1,7 @@ +# NOTE: In order to write comment and edit labels, this script requires workflows with write permissions. +# It should not use any untrusted third party code, or any code checked into the repository itself +# as that could indirectly grant PRs the ability to edit labels and comments on PRs. + import os import git import requests diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 2b8c4e3ce1c..74434f0d2c4 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -12,8 +12,8 @@ jobs: fetch-depth: 0 - run: | - # Make sure the script is unmodified - echo "8be2d295e8436ce557acc8a4d3b82a639913ae65de0d1a76871f21359b4e8d9f .github/workflows/tagbot.py"|sha256sum --check --status + # Make sure the script is unmodified as it runs with write permissions + echo "f525f362a99f13764791185da4d45959a632ef54e3b6b865461dabddb1b1df34 .github/workflows/tagbot.py"|sha256sum --check --status - name: set up Python uses: actions/setup-python@v5 From 36587809c1944bec0ffd752cb522a5c7af2fa5a4 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 1 Nov 2024 17:08:49 +0100 Subject: [PATCH 384/524] fixed coding style --- .../easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb index 6b256f6e3df..5c3ef3f7b45 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb @@ -14,9 +14,9 @@ toolchain = {'name': 'GCC', 'version': '13.3.0'} source_urls = ['https://%(namelower)s.freedesktop.org/src/%(namelower)s'] sources = [SOURCELOWER_TAR_XZ] patches = ['%(name)s-1.24_fix_bad_suid.patch'] -checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', # gstreamer-1.24.8.tar.xz - 'e40c8b195cc9d44f2d9b92e57608e097ef8dac6fa761c5610fcb836f88610cb1', # %(name)s-1.24_fix_bad_suid.patch -] +checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', # gstreamer-1.24.8.tar.xz + 'e40c8b195cc9d44f2d9b92e57608e097ef8dac6fa761c5610fcb836f88610cb1', # %(name)s-1.24_fix_bad_suid.patch + ] builddependencies = [ ('Meson', '1.4.0'), From 2ac4ad42ab03137535f805e62cf886aee5216219 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 13:53:48 +0100 Subject: [PATCH 385/524] Try using conditional workflow based on if tagbot is modified. --- .github/workflows/tagbot.yml | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 74434f0d2c4..a1b7f673e1c 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -11,9 +11,25 @@ jobs: with: fetch-depth: 0 - - run: | - # Make sure the script is unmodified as it runs with write permissions - echo "f525f362a99f13764791185da4d45959a632ef54e3b6b865461dabddb1b1df34 .github/workflows/tagbot.py"|sha256sum --check --status + - name: Check if file has changed + run: | + if git diff --name-only origin/${{ github.event.pull_request.base.ref }}...HEAD | grep -q .github/workflows/tagbot.py; then + echo "tagbot_modified=true" >> $GITHUB_ENV + else + echo "tagbot_modified=false" >> $GITHUB_ENV + fi + + - name: Post warning comment + if: env.file_modified == 'true' + uses: actions/github-script@v7 + with: + script: | + github.rest.issues.createComment({ + issue_number: ${{ github.event.pull_request.number }}, + owner: context.repo.owner, + repo: context.repo.repo, + body: "⚠️ Warning: The tagbot.py file has been modified. Please review changes carefully." + }) - name: set up Python uses: actions/setup-python@v5 @@ -24,6 +40,7 @@ jobs: run: pip install gitpython requests - name: Tag and comment + if: env.tagbot_modified == 'false' env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: python .github/workflows/tagbot.py From 3aed346a76bf91727ac1db30358eb4a4ef2b5973 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 20:26:34 +0100 Subject: [PATCH 386/524] Add debug printout temporarily --- .github/workflows/tagbot.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 649dd1dd828..3c02574468c 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -64,6 +64,9 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) +print('env:', os.environ) +print('data:', data) + pr_number = data['pull_request']['number'] print("PR number:", pr_number) From 910b530d0d9039dddeb3f407f41694fd597c8e14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 20:51:02 +0100 Subject: [PATCH 387/524] Add checkout of PR commit --- .github/workflows/tagbot.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index a1b7f673e1c..dd0197456f5 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -9,6 +9,7 @@ jobs: steps: - uses: actions/checkout@v4 with: + ref: "${{ github.event.pull_request.merge_commit_sha }}" fetch-depth: 0 - name: Check if file has changed From 29232d7dd63da65f3bd56de7dc9b631821194daa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 21:17:38 +0100 Subject: [PATCH 388/524] Fix tagbot.py to use merge commit sha when diffing --- .github/workflows/tagbot.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 3c02574468c..e5348382bf7 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -59,26 +59,22 @@ def pr_ecs(pr_diff): token = os.getenv("GH_TOKEN") repo = os.getenv("GITHUB_REPOSITORY") base_branch_name = os.getenv("GITHUB_BASE_REF") -pr_ref_name = os.getenv("GITHUB_REF_NAME") with open(event_path) as f: data = json.load(f) -print('env:', os.environ) -print('data:', data) - pr_number = data['pull_request']['number'] +merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) print("Repo:", repo) print("Base branch name:", base_branch_name) -print("PR ref:", pr_ref_name) +print("Merge commit ref:", ) gitrepo = git.Repo(".") - target_commit = gitrepo.commit('origin/' + base_branch_name) -pr_commit = gitrepo.commit('pull/' + pr_ref_name) +pr_commit = gitrepo.commit(merge_commit_sha) pr_diff = target_commit.diff(pr_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) From 3572045db84852caef4e2a1ea007b3c3f9052cdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 21:44:26 +0100 Subject: [PATCH 389/524] Fix typo --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index dd0197456f5..e15a06ba608 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -21,7 +21,7 @@ jobs: fi - name: Post warning comment - if: env.file_modified == 'true' + if: env.tagbot_modified == 'true' uses: actions/github-script@v7 with: script: | From 61d3f6e56bd9749b5942a33f6dc80868d0e27ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 22:41:19 +0100 Subject: [PATCH 390/524] Fix missing printout in tagbot --- .github/workflows/tagbot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index e5348382bf7..5ab67361e92 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -69,7 +69,7 @@ def pr_ecs(pr_diff): print("PR number:", pr_number) print("Repo:", repo) print("Base branch name:", base_branch_name) -print("Merge commit ref:", ) +print("Merge commit ref:", merge_commit_sha) gitrepo = git.Repo(".") From 229223c423fec9750f7b32853fbe53980830eede Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 23:05:46 +0100 Subject: [PATCH 391/524] Add additional label for workflow changes, to highlight for reviewers --- .github/workflows/tagbot.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 5ab67361e92..944571d8e45 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -78,9 +78,11 @@ def pr_ecs(pr_diff): pr_diff = target_commit.diff(pr_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) +modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) print("Changed ECs:", changed_ecs) print("Newly added ECs:", new_ecs) +print("Modified workflow:", modified_workflow) new_software = 0 updated_software = 0 @@ -125,9 +127,14 @@ def pr_ecs(pr_diff): print("Adjusting labels") current_labels = [label['name'] for label in data['pull_request']['labels']] +label_checks = [(changed_ecs, 'change'), + (new_software, 'new'), + (updated_software, 'update'), + (modified_workflow, 'workflow')] + labels_add = [] labels_del = [] -for condition, label in [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]: +for condition, label in label_checks: if condition and label not in current_labels: labels_add.append(label) elif not condition and label in current_labels: From 02bfe0a45564d81344b68e903d91831c1905e4e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:13:17 +0100 Subject: [PATCH 392/524] Rework yml, only run when no merge conflict, fix possible security hole --- .github/workflows/tagbot.py | 17 ++--------------- .github/workflows/tagbot.yml | 29 +++++++---------------------- 2 files changed, 9 insertions(+), 37 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 944571d8e45..51c18184387 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -6,7 +6,6 @@ import git import requests import json -import difflib from datetime import datetime from pathlib import Path @@ -31,17 +30,6 @@ def similar_easyconfigs(repo, new_file): return sort_by_added_date(repo, possible_neighbours) -def diff(old, new): - with open(old, 'r') as old_file, open(new, 'r') as new_file: - old_lines = list(old_file) - new_lines = list(new_file) - return ''.join(difflib.unified_diff( - old_lines, - new_lines, - fromfile=str(old), - tofile=str(new))) - - def pr_ecs(pr_diff): new_ecs = [] changed_ecs = [] @@ -67,11 +55,10 @@ def pr_ecs(pr_diff): merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) -print("Repo:", repo) print("Base branch name:", base_branch_name) print("Merge commit ref:", merge_commit_sha) -gitrepo = git.Repo(".") +gitrepo = git.Repo("pr") target_commit = gitrepo.commit('origin/' + base_branch_name) pr_commit = gitrepo.commit(merge_commit_sha) @@ -121,7 +108,7 @@ def pr_ecs(pr_diff): comment += f'Diff against {neighbour.name}\n\n' comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' comment += '```diff\n' - comment += diff(neighbour, new_file) + comment += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}') comment += '```\n\n\n' print("Adjusting labels") diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index e15a06ba608..9aaa8084e6a 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -3,35 +3,21 @@ on: [pull_request_target] jobs: tagbot: + if: github.event.pull_request.merge_commit_sha runs-on: ubuntu-24.04 permissions: pull-requests: write steps: - - uses: actions/checkout@v4 + - name: Checkout base branch for workflow scripts + uses: actions/checkout@v4 + + - name: Checkout PR for computing diff + uses: actions/checkout@v4 with: ref: "${{ github.event.pull_request.merge_commit_sha }}" + path: 'pr' fetch-depth: 0 - - name: Check if file has changed - run: | - if git diff --name-only origin/${{ github.event.pull_request.base.ref }}...HEAD | grep -q .github/workflows/tagbot.py; then - echo "tagbot_modified=true" >> $GITHUB_ENV - else - echo "tagbot_modified=false" >> $GITHUB_ENV - fi - - - name: Post warning comment - if: env.tagbot_modified == 'true' - uses: actions/github-script@v7 - with: - script: | - github.rest.issues.createComment({ - issue_number: ${{ github.event.pull_request.number }}, - owner: context.repo.owner, - repo: context.repo.repo, - body: "⚠️ Warning: The tagbot.py file has been modified. Please review changes carefully." - }) - - name: set up Python uses: actions/setup-python@v5 with: @@ -41,7 +27,6 @@ jobs: run: pip install gitpython requests - name: Tag and comment - if: env.tagbot_modified == 'false' env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: python .github/workflows/tagbot.py From f8180eacaef082a134383ca5856fe094b7fdf8ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:45:07 +0100 Subject: [PATCH 393/524] Add target commit sha for debuggin --- .github/workflows/tagbot.py | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 51c18184387..4d4defbaaf2 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -61,6 +61,7 @@ def pr_ecs(pr_diff): gitrepo = git.Repo("pr") target_commit = gitrepo.commit('origin/' + base_branch_name) +print("Target commit ref:", target_commit) pr_commit = gitrepo.commit(merge_commit_sha) pr_diff = target_commit.diff(pr_commit) From 8668891865975619ba074e290564a6f1fb078ecf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:50:48 +0100 Subject: [PATCH 394/524] Print out github event data for debugging --- .github/workflows/tagbot.py | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 4d4defbaaf2..ff77576bd09 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -51,6 +51,7 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) +print(data) pr_number = data['pull_request']['number'] merge_commit_sha = data['pull_request']['merge_commit_sha'] From b2fb3c9417c6cad5e1628b57c8870935d5d32e40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:11:05 +0100 Subject: [PATCH 395/524] Switch to manually attempting merge due to github race condition with pull_request_target --- .github/workflows/tagbot.py | 23 ++++++++++++----------- .github/workflows/tagbot.yml | 17 +++++++++++++++-- 2 files changed, 27 insertions(+), 13 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index ff77576bd09..937b5b86313 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -15,8 +15,7 @@ def get_first_commit_date(repo, file_path): if commits: return commits[-1].committed_date else: - print(f"{file_path} has no commit info, putting it last") - return datetime.datetime.min + raise ValueError(f'{file_path} has no commit info, this should not happen') def sort_by_added_date(repo, file_paths): @@ -43,28 +42,30 @@ def pr_ecs(pr_diff): GITHUB_API_URL = 'https://api.github.com' -event_path = os.getenv("GITHUB_EVENT_PATH") -token = os.getenv("GH_TOKEN") -repo = os.getenv("GITHUB_REPOSITORY") -base_branch_name = os.getenv("GITHUB_BASE_REF") +event_path = os.getenv('GITHUB_EVENT_PATH') +token = os.getenv('GH_TOKEN') +repo = os.getenv('GITHUB_REPOSITORY') +base_branch_name = os.getenv('GITHUB_BASE_REF') with open(event_path) as f: data = json.load(f) print(data) pr_number = data['pull_request']['number'] -merge_commit_sha = data['pull_request']['merge_commit_sha'] +# Can't rely on merge_commit_sha for pull_request_target as it might be outdated +# merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) print("Base branch name:", base_branch_name) -print("Merge commit ref:", merge_commit_sha) -gitrepo = git.Repo("pr") +# Change into "pr" checkout directory to allow diffs and glob to work on the same content +os.chdir('pr') +gitrepo = git.Repo('.') target_commit = gitrepo.commit('origin/' + base_branch_name) print("Target commit ref:", target_commit) -pr_commit = gitrepo.commit(merge_commit_sha) -pr_diff = target_commit.diff(pr_commit) +merge_commit = gitrepo.head.commit +pr_diff = target_commit.diff(merge_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9aaa8084e6a..9001819d04f 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -3,7 +3,8 @@ on: [pull_request_target] jobs: tagbot: - if: github.event.pull_request.merge_commit_sha + # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target + # does not wait github mergability check, and the value is outdated. runs-on: ubuntu-24.04 permissions: pull-requests: write @@ -14,9 +15,21 @@ jobs: - name: Checkout PR for computing diff uses: actions/checkout@v4 with: - ref: "${{ github.event.pull_request.merge_commit_sha }}" + ref: "${{ github.event.pull_request.head.sha }}" path: 'pr' fetch-depth: 0 + + - name: Attempt Merge + id: merge + run: | + git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + continue-on-error: true + + - name: Check merge result + if: steps.merge.outcome == 'failure' + run: | + echo "Merge conflict detected, failing job." + exit 1 - name: set up Python uses: actions/setup-python@v5 From 9772d1416c959c1a5ed2071791a50ffc04ec0689 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:31:18 +0100 Subject: [PATCH 396/524] Add concurrency to prevent conflicting tags/comments --- .github/workflows/tagbot.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9001819d04f..d47eb812c22 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -1,6 +1,10 @@ name: Tagbot on: [pull_request_target] +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target From baaa8ba5b5e6b44556909e46f4123961074380be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:35:17 +0100 Subject: [PATCH 397/524] Remove unsused import --- .github/workflows/tagbot.py | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 937b5b86313..e16f10c2411 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -6,7 +6,6 @@ import git import requests import json -from datetime import datetime from pathlib import Path From 58debaac6d668361d92296301a30425473a7c3b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:46:01 +0100 Subject: [PATCH 398/524] Add quotes around concurrency group --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index d47eb812c22..7b7184e3415 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -2,7 +2,7 @@ name: Tagbot on: [pull_request_target] concurrency: - group: ${{ github.workflow }}-${{ github.ref }} + group: "${{ github.workflow }}-${{ github.ref }}" cancel-in-progress: true jobs: From 16ac316aafebef4b6da77c366b7a1f317dc046b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:50:56 +0100 Subject: [PATCH 399/524] Fix indentation --- .github/workflows/tagbot.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 7b7184e3415..c7b929a10da 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -23,17 +23,17 @@ jobs: path: 'pr' fetch-depth: 0 - - name: Attempt Merge - id: merge - run: | - git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} - continue-on-error: true - - - name: Check merge result - if: steps.merge.outcome == 'failure' - run: | - echo "Merge conflict detected, failing job." - exit 1 + - name: Attempt Merge + id: merge + run: | + git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + continue-on-error: true + + - name: Check merge result + if: steps.merge.outcome == 'failure' + run: | + echo "Merge conflict detected, failing job." + exit 1 - name: set up Python uses: actions/setup-python@v5 From b0f49b92cd5a0e306ef5f9924340a89d9e4c7c45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 22:33:44 +0100 Subject: [PATCH 400/524] Make steps more explicit, perform merge in pr subdir --- .github/workflows/tagbot.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index c7b929a10da..9aacbf0df08 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -16,7 +16,7 @@ jobs: - name: Checkout base branch for workflow scripts uses: actions/checkout@v4 - - name: Checkout PR for computing diff + - name: Checkout PR for computing diff into "pr" subdirectory uses: actions/checkout@v4 with: ref: "${{ github.event.pull_request.head.sha }}" @@ -26,10 +26,11 @@ jobs: - name: Attempt Merge id: merge run: | + cd pr git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true - - name: Check merge result + - name: Abort if merge failed if: steps.merge.outcome == 'failure' run: | echo "Merge conflict detected, failing job." From 51dd49e48c290a937e9ce72b7042a74c6c472e8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 23:52:14 +0100 Subject: [PATCH 401/524] Add missing linebreak on code blocks --- .github/workflows/tagbot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index e16f10c2411..a46ae810cfe 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -111,7 +111,7 @@ def pr_ecs(pr_diff): comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' comment += '```diff\n' comment += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}') - comment += '```\n\n\n' + comment += '\n```\n\n\n' print("Adjusting labels") current_labels = [label['name'] for label in data['pull_request']['labels']] From e9f42feb6da37054cbf16645f7f33337d51c7dc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 23:55:40 +0100 Subject: [PATCH 402/524] Make stdoutput nicer, display merge commit sha --- .github/workflows/tagbot.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index a46ae810cfe..792f457c197 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -64,13 +64,15 @@ def pr_ecs(pr_diff): target_commit = gitrepo.commit('origin/' + base_branch_name) print("Target commit ref:", target_commit) merge_commit = gitrepo.head.commit +print("Merge commit:", merge_commit) pr_diff = target_commit.diff(merge_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) -print("Changed ECs:", changed_ecs) -print("Newly added ECs:", new_ecs) + +print("Changed ECs:", ', '.join(changed_ecs)) +print("Newly added ECs:", ', '.join(new_ecs)) print("Modified workflow:", modified_workflow) new_software = 0 From 40ca1dd72732a0257d3d9d3692f571dbd186a284 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 00:04:01 +0100 Subject: [PATCH 403/524] Add git name/email for temporary merge test --- .github/workflows/tagbot.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9aacbf0df08..e14752f1f86 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -9,6 +9,7 @@ jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target # does not wait github mergability check, and the value is outdated. + # Instead we merge manually in a temporary subdir "pr" runs-on: ubuntu-24.04 permissions: pull-requests: write @@ -23,12 +24,14 @@ jobs: path: 'pr' fetch-depth: 0 - - name: Attempt Merge + - name: Attempt test merge id: merge run: | - cd pr + git config user.name "github-workflow" + git config user.email "github-workflow@github.com" git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true + working-directory: pr - name: Abort if merge failed if: steps.merge.outcome == 'failure' From 4c021b4a719ae9fc961bc347f962c8243d17e4f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 00:14:30 +0100 Subject: [PATCH 404/524] Fix string conversion for printout --- .github/workflows/tagbot.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 792f457c197..d9a16320aa5 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -71,8 +71,8 @@ def pr_ecs(pr_diff): modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) -print("Changed ECs:", ', '.join(changed_ecs)) -print("Newly added ECs:", ', '.join(new_ecs)) +print("Changed ECs:", ', '.join(str(p) for p in changed_ecs)) +print("Newly added ECs:", ', '.join(str(p) for p in new_ecs)) print("Modified workflow:", modified_workflow) new_software = 0 From 0318112770a7c65e9c085869936f8b9a3140886e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 02:01:05 +0100 Subject: [PATCH 405/524] Drop very verbose debug output of event data --- .github/workflows/tagbot.py | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index d9a16320aa5..26472f8bcbd 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -49,7 +49,6 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) -print(data) pr_number = data['pull_request']['number'] # Can't rely on merge_commit_sha for pull_request_target as it might be outdated # merge_commit_sha = data['pull_request']['merge_commit_sha'] From 3b69ab8fd9339e354d595ebe0cccb50666352bc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 4 Nov 2024 11:35:33 +0100 Subject: [PATCH 406/524] adding easyconfigs: Stacks-2.68-foss-2023a.eb --- .../s/Stacks/Stacks-2.68-foss-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb new file mode 100644 index 00000000000..f5c8c3b976d --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.68' + +homepage = 'https://catchenlab.life.illinois.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650'] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From 3d955bff8243eddcd001344b23cef789e7f676c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 4 Nov 2024 12:09:58 +0100 Subject: [PATCH 407/524] adding easyconfigs: mosdepth-0.3.9-GCC-12.3.0.eb, Nim-2.2.0-GCCcore-12.3.0.eb --- .../m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb | 48 +++++++++++++++++++ .../n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb | 17 +++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..8fcad4de92b --- /dev/null +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'Binary' + +name = 'mosdepth' +version = '0.3.9' +local_hts_nim_ver = '0.3.25' + +homepage = 'https://github.com/brentp/mosdepth' +description = "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/brentp/hts-nim/archive/'], + 'download_filename': 'v%s.tar.gz' % local_hts_nim_ver, + 'filename': 'hts-nim-%s.tar.gz' % local_hts_nim_ver, + }, + { + 'source_urls': ['https://github.com/brentp/mosdepth/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = [ + {'hts-nim-0.3.25.tar.gz': 'b13b9bb5aa567a69bf17547aadbbd39e37beb4f71a28f267b83dfea9ea4d05e8'}, + {'mosdepth-0.3.9.tar.gz': '9171ea9a6ddaccd0091db5b85fa9e6cb79516bbe005c47ffc8dcfe49c978eb69'}, +] + +dependencies = [ + ('Nim', '2.2.0'), + ('HTSlib', '1.18'), + ('PCRE', '8.45'), +] + +extract_sources = True + +install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" + +sanity_check_paths = { + 'files': ['bin/mosdepth'], + 'dirs': [], +} + +sanity_check_commands = ["mosdepth --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2214b1c9493 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '2.2.0' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ce9842849c9760e487ecdd1cdadf7c0f2844cafae605401c7c72ae257644893c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libreadline', '8.2')] + +moduleclass = 'lang' From cbb32e4b28f652c86f636f62f110e60b35ab6864 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 4 Nov 2024 14:05:43 +0100 Subject: [PATCH 408/524] use upstream name for dask_ml extension in Dask-ML-2024.4.4-foss-2023a.eb --- .../easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb index fd593a4bb09..f4bdf4425ae 100644 --- a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -42,9 +42,7 @@ exts_list = [ ('packaging', '24.1', { 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], }), - (name, version, { - 'modulename': 'dask_ml', - 'sources': ['dask_ml-%(version)s.tar.gz'], + ('dask_ml', version, { 'checksums': ['7956910a49e1e31944280fdb311adf245da11ef410d67deb7a05c67c7d0c4498'], }), ] From 7b99beb7e8cf81b66041e2fb0d5c266cc360b0f6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 4 Nov 2024 19:18:22 +0100 Subject: [PATCH 409/524] adding easyconfigs: mustache-hic-1.3.3-foss-2023b.eb, hic-straw-1.3.1-foss-2023b.eb, cooler-0.10.2-foss-2023b.eb, multiprocess-0.70.16-gfbf-2023b.eb --- .../c/cooler/cooler-0.10.2-foss-2023b.eb | 46 +++++++++++++++++++ .../h/hic-straw/hic-straw-1.3.1-foss-2023b.eb | 29 ++++++++++++ .../multiprocess-0.70.16-gfbf-2023b.eb | 24 ++++++++++ .../mustache-hic-1.3.3-foss-2023b.eb | 38 +++++++++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb create mode 100644 easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb new file mode 100644 index 00000000000..f092666e99d --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.10.2' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('PyYAML', '6.0.1'), + ('pyfaidx', '0.8.1.1'), + ('dill', '0.3.8'), + ('multiprocess', '0.70.16'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '1.0.0', { + 'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'], + }), + ('cytoolz', '1.0.0', { + 'checksums': ['eb453b30182152f9917a5189b7d99046b6ce90cdf8aeb0feff4b2683e600defd'], + }), + (name, version, { + 'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb new file mode 100644 index 00000000000..4a9b159e99b --- /dev/null +++ b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'hic-straw' +version = '1.3.1' + +homepage = 'https://github.com/aidenlab/straw' +description = "Straw is a library which allows rapid streaming of contact data from .hic files." + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fb0f878127f6b1d096303c67793477c83fddf3f4a1a8e29a9d92952634989876'] + +builddependencies = [('pybind11', '2.11.1')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('cURL', '8.3.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'hicstraw'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb new file mode 100644 index 00000000000..956b6c8610d --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.16' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] + +dependencies = [ + ('Python', '3.11.5'), + ('dill', '0.3.8'), + ('Arrow', '16.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb b/easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb new file mode 100644 index 00000000000..2eb0c9676c0 --- /dev/null +++ b/easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'mustache-hic' +version = '1.3.3' + +homepage = 'https://github.com/ay-lab/mustache' +description = """Mustache (Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using +Scale-Space Representation) is a tool for multi-scale detection of chromatin loops from Hi-C and Micro-C +contact maps in high resolutions (10kbp all the way to 500bp and even more). +Mustache uses recent technical advances in scale-space theory in +Computer Vision to detect chromatin loops caused by interaction of DNA segments with a variable size.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [{'download_filename': 'mustache_hic-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['fd7cca927e36145bf6e43903a79c3222ecfeeb497c8f57657d7647ec6eee5a6b'] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('HDF5', '1.14.3'), + ('cooler', '0.10.2'), + ('statsmodels', '0.14.1'), + ('hic-straw', '1.3.1'), +] + +# delete pathlib dependency from setup.py +preinstallopts = "sed -i 's/pathlib//' setup.py && " + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +options = {'modulename': 'mustache'} + +moduleclass = 'ai' From a39ea4028ef0d9a6cbbe14bf3a3e00e1f604bc85 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 5 Nov 2024 09:59:29 +0100 Subject: [PATCH 410/524] resolve style error --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 867969666e1..7c85236b0a4 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -40,7 +40,7 @@ dependencies = [ ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), ('Perl-bundle-CPAN', '5.36.1'), - ('DB', '18.1.40'), # for DB_File + ('DB', '18.1.40'), # for DB_File ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('BLAST+', '2.14.1'), From 35c11c91b108a892372f64dc7b60392312f21cae Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 5 Nov 2024 14:45:57 +0100 Subject: [PATCH 411/524] adding easyconfigs: Porechop-0.2.4-20240119-GCCcore-12.3.0.eb --- .../Porechop-0.2.4-20240119-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e1dfa5d567c --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4-20240119' +local_commit = 'd2e77c6' + +homepage = 'https://github.com/dehui333/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dehui333/Porechop/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From d44547734a443238653d586db01553b1edf0f38c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 5 Nov 2024 15:36:01 +0100 Subject: [PATCH 412/524] simplifying and add description --- .../o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb index 8b0c54b4248..f205e063da9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb @@ -42,9 +42,14 @@ builddependencies = [ ('Python', '3.11.5'), ] +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " -testopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " -installopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 From 2f6468662289f25498348091851ca3732f2ef54b Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 5 Nov 2024 16:08:35 +0000 Subject: [PATCH 413/524] adding easyconfigs: RAxML-NG-1.2.2-GCC-13.2.0.eb --- .../r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..e4a2c353676 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb @@ -0,0 +1,44 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.2.2' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +sources = [{ + 'filename': '%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GMP', '6.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/raxml-ng'], + 'dirs': [], +} + +sanity_check_commands = ["raxml-ng --help"] + +moduleclass = 'bio' From 9c0f59f60b9da28c4463c991fc62abbac301569a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 5 Nov 2024 16:35:11 +0000 Subject: [PATCH 414/524] adding easyconfigs: MAFFT-7.526-GCC-13.2.0-with-extensions.eb --- .../MAFFT-7.526-GCC-13.2.0-with-extensions.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb new file mode 100644 index 00000000000..175e1013f56 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) +# Thomas Eylenbosch (Gluo NV) +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.526' +versionsuffix = '-with-extensions' +local_commit = 'ee9799916df6a5d5103d46d54933f8eb6d28e244' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://gitlab.com/sysimm/mafft/-/archive/v%(version)s/'], + 'sources': ['mafft-%(version)s.tar.gz'], + 'checksums': ['6f536ec957b76f4e38e869d935d6626d318361ef8ee95e71c795b924f639ee10'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/core' % local_commit, + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/extensions' % local_commit, + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' From ca81bd89d82cb032dc3723f64313360e063f96fd Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 5 Nov 2024 19:51:18 +0100 Subject: [PATCH 415/524] Update .github/workflows/tagbot.yml --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index e14752f1f86..6a518cbe03d 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -8,7 +8,7 @@ concurrency: jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target - # does not wait github mergability check, and the value is outdated. + # does not wait for github mergability check, and the value is outdated. # Instead we merge manually in a temporary subdir "pr" runs-on: ubuntu-24.04 permissions: From 5f96bd16878e6b8efe273a4be9d8ed1b4b11f2c4 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 6 Nov 2024 09:36:30 +0000 Subject: [PATCH 416/524] adding easyconfigs: librsvg-2.58.0-GCCcore-12.3.0.eb --- .../librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1391bcb955e --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.58.0' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d7c444a926406b59790be0deae196e18ed26059da573fa1aa9ec9ca7658a559c'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('cairo', '1.17.8'), + ('freetype', '2.13.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('HarfBuzz', '5.3.1'), + ('Pango', '1.50.14'), + ('GObject-Introspection', '1.76.1'), +] + +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' From 047308f8faa9dc9094b065d96f49eb5cebe2b958 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 6 Nov 2024 11:46:45 +0100 Subject: [PATCH 417/524] Update URL --- easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb index 09c315d4561..081fb8af634 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb @@ -9,7 +9,10 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe toolchain = {'name': 'foss', 'version': '2024a'} toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} -source_urls = ['https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/946183/'] +source_urls = [ + 'https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/946183/', + 'https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/342056/', +] sources = ['NAMD_%(version)s_Source.tar.gz'] patches = ['NAMD-3.0_fix_hwloc_build.patch'] From fd5dcd3eb38f36c56fb8d4b2fe3cf5476cedf841 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 6 Nov 2024 14:44:32 +0100 Subject: [PATCH 418/524] adding easyconfigs: BindCraft-1.1.0-foss-2023a.eb, PyRosetta-4.release-387-gompi-2023a.eb, dm-haiku-0.0.13-foss-2023a.eb --- .../b/BindCraft/BindCraft-1.1.0-foss-2023a.eb | 89 +++++++++++++++++++ .../d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb | 34 +++++++ .../PyRosetta-4.release-387-gompi-2023a.eb | 38 ++++++++ 3 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..49345e486d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -0,0 +1,89 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25'), + ('dm-haiku', '0.0.13'), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2'), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('hatchling', '1.18.0'), + ('Flax', '0.8.4'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb new file mode 100644 index 00000000000..532f9092e79 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.13' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), # required by jmp, also provides absl-py +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'], + }), + ('dm_haiku', version, { + 'modulename': 'haiku', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb new file mode 100644 index 00000000000..c37102d5a81 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-387' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From aaa25360d0ea1e4f47af2ea7736b72b6d07e1c9e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 Nov 2024 15:26:20 +0100 Subject: [PATCH 419/524] {numlib}[GCC-13.3.0] OpenBLAS 0.3.27 sequential with 64 bit interface --- .../OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb new file mode 100644 index 00000000000..5527c667f66 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb @@ -0,0 +1,60 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.12.3'), +] + +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 628a7ebd15550dba4d76f51e2ba83899b23fe639 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 6 Nov 2024 15:48:25 +0100 Subject: [PATCH 420/524] Fix tagbot concurrency group Can't use github.ref when using pull_request_target, since that value also points to base ref. --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 6a518cbe03d..811599999fd 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -2,7 +2,7 @@ name: Tagbot on: [pull_request_target] concurrency: - group: "${{ github.workflow }}-${{ github.ref }}" + group: "${{ github.workflow }}-${{ github.event.pull_request.number }}" cancel-in-progress: true jobs: From 219e64c2fc8d572424b6c77defe472ef6671037c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 6 Nov 2024 17:22:04 +0100 Subject: [PATCH 421/524] Actually perform temporary merge in checkout to determine PR changes --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 6a518cbe03d..958a776d46a 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -29,7 +29,7 @@ jobs: run: | git config user.name "github-workflow" git config user.email "github-workflow@github.com" - git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + git merge --no-edit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true working-directory: pr From 3765d5e4c20c9b08d3c5ac2472ed58a98bd228b8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 17:37:12 +0100 Subject: [PATCH 422/524] adding easyconfigs: GPAW-24.6.0-foss-2024a.eb, ASE-3.23.0-gfbf-2024a.eb, libvdwxc-0.4.0-foss-2024a.eb, spglib-python-2.5.0-gfbf-2024a.eb --- .../a/ASE/ASE-3.23.0-gfbf-2024a.eb | 48 ++++++++++++++++++ .../g/GPAW/GPAW-24.6.0-foss-2024a.eb | 50 +++++++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb | 27 ++++++++++ .../spglib-python-2.5.0-gfbf-2024a.eb | 37 ++++++++++++++ 4 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb new file mode 100644 index 00000000000..472ebbb24b2 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('Flask', '3.0.3'), + ('matplotlib', '3.9.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb new file mode 100644 index 00000000000..9b8721280c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('ASE', '3.23.0'), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2024.05.001'), + ('PyYAML', '6.0.2'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb new file mode 100644 index 00000000000..2fd7d01390f --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb new file mode 100644 index 00000000000..a6954207aa7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('scikit-build-core', '0.10.6') +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('spglib', version, { + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' From d1503c91f54c7580d7eea72e06e56deaa991ecb7 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:06:09 +0100 Subject: [PATCH 423/524] Add libxc from #21796. Update webpage in libvdwxc --- .../l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb | 2 +- .../l/libxc/libxc-6.2.2-GCC-13.3.0.eb | 52 +++++++++++++++++++ 2 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb index 2fd7d01390f..de1dca5e394 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..9e4de5e8082 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://gitlab.com/%(name)s/%(name)s/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [ + ('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc', + 'd1b65ef74615a1e539d87a0e6662f04baf3a2316706b4e2e686da3193b26b20f'), +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' From 3e35d8a5c170dedfdd24f6825f1c9537a08b5bf8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:20:41 +0100 Subject: [PATCH 424/524] Update libvdwxc webpage as old URL has been taken over by evildoers. --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb index df2d4d407fe..411ee1867d8 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.3.2' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb index 99914532433..b750b9a414f 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" From f2a65af3049b3a71f82a77a7c402d2835ecbfc6a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:25:25 +0100 Subject: [PATCH 425/524] Update libvdwxc webpage as old URL has been taken over by evildoers. --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb index c9f93a8ff91..a04a99002a9 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb index c6769e53157..dd9797af734 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb index 9dee6b6ef26..0e414c5d729 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb index eb7dd54a47d..843a00aaac2 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb index c5a0fad835b..1050fbf314f 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb index b1785ef119b..3b14a5ca707 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb index 9cf45cc3abe..7c8c009c9d0 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 751488a0728..a610d3ec773 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb index cdc3abd5a19..e137148b85c 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb index c8c0d2a8644..5df0f660f1d 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" From 52fc537edea8b8e0c0b32b90a3b89cdc231fafe7 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 7 Nov 2024 12:53:38 +0100 Subject: [PATCH 426/524] add missing link to Library Path for Faiss --- .../easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb index a55db18bfc6..1a9b1727bba 100644 --- a/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb @@ -60,6 +60,8 @@ postinstallcmds = [ ]) ] +modextrapaths = {'LD_LIBRARY_PATH': "lib/python%(pyshortver)s/site-packages/faiss"} + sanity_check_paths = { 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], 'dirs': ['include/%(namelower)s', 'lib/python%(pyshortver)s/site-packages/%(namelower)s'], From f837d974757a4bcf8813501477d2bdcc939b624f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 7 Nov 2024 13:12:07 +0100 Subject: [PATCH 427/524] adding easyconfigs: GROMACS-LS-2016.3-foss-2023a.eb, MDStress-20191228-gfbf-2023a.eb and patches: GROMACS-LS-2016.3_fix_typo.patch, MDStress-20191228_use_external_voro++_and_EB_lapack.patch --- .../GROMACS-LS-2016.3-foss-2023a.eb | 49 ++++++++++++ .../GROMACS-LS-2016.3_fix_typo.patch | 38 +++++++++ .../MDStress/MDStress-20191228-gfbf-2023a.eb | 41 ++++++++++ ...28_use_external_voro++_and_EB_lapack.patch | 80 +++++++++++++++++++ 4 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch create mode 100644 easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb new file mode 100644 index 00000000000..e47a07b97f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'EB_GROMACS' + +name = 'GROMACS-LS' +version = '2016.3' + +homepage = 'https://vanegaslab.org/software' +description = """ +GROMACS-LS and the MDStress library enable the calculation of local +stress fields from molecular dynamics simulations. + +This is a double precision only CPU only build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['gromacs-ls-2016.3-12282019.tar.gz'] +patches = [ + 'GROMACS-LS-2016.3_fix_typo.patch', +] +checksums = [ + {'gromacs-ls-2016.3-12282019.tar.gz': '20f4d4f255800432be188abe41b7fec923cacc5fc895914b3beac0808ddf1919'}, + {'GROMACS-LS-2016.3_fix_typo.patch': '4b9945476405a358bc64784984c51f08ab1aa3a598fb981b2dad8e0c61665fe0'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('MDStress', '20191228'), +] + +# GROMACS-LS can only be built with double precision +single_precision = False + +# GROMACS-LS can only handle hwloc version < 2 +configopts = '-DGMX_HWLOC=OFF' + +# The tests have not been rewritten to handle the mdstress changes +skipsteps = ['test'] + +sanity_check_paths = { + 'files': ['bin/gmx_LS', 'lib/libgromacs_LS.a'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch new file mode 100644 index 00000000000..2529da617ed --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch @@ -0,0 +1,38 @@ +Fix a couple of smaller problems + +Åke Sandgren, 2024-11-07 +diff -ru gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake +--- gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake 2019-12-28 15:42:21.000000000 +0100 ++++ gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake 2024-11-07 10:45:40.060210373 +0100 +@@ -49,7 +49,7 @@ + elseif(CYGWIN) + set(CXX11_CXX_FLAG "-std=gnu++0x") #required for strdup + else() +- set(CXX11_CXX_FLAG "-std=c++0x") ++ set(CXX11_CXX_FLAG "-std=c++11") + endif() + CHECK_CXX_COMPILER_FLAG("${CXX11_CXX_FLAG}" CXXFLAG_STD_CXX0X) + if(NOT CXXFLAG_STD_CXX0X) +diff -ru gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp +--- gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp 2019-12-28 15:42:28.000000000 +0100 ++++ gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp 2024-11-07 10:55:06.668206192 +0100 +@@ -54,6 +54,7 @@ + + #include + #include ++#include + + #include "gromacs/commandline/filenm.h" + #include "gromacs/domdec/domdec.h" +diff -ru gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp gromacs-ls-2016.3/src/programs/mdrun/runner.cpp +--- gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp 2019-12-28 15:42:30.000000000 +0100 ++++ gromacs-ls-2016.3/src/programs/mdrun/runner.cpp 2024-11-07 10:33:22.588969615 +0100 +@@ -175,7 +175,7 @@ + int localsspatialatom; + int localsdispcor; + int localspbc; +- real localsmindihang; ++ real localsmindihangle; + unsigned long Flags; + }; + diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb new file mode 100644 index 00000000000..7be20fe7e5b --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'MDStress' +version = '20191228' + +homepage = 'https://vanegaslab.org/software' +description = """MDStress library enable the calculation of local stress +fields from molecular dynamics simulations""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['mdstress-library-12282019.tar.gz'] +patches = [ + 'MDStress-20191228_use_external_voro++_and_EB_lapack.patch', +] +checksums = [ + {'mdstress-library-12282019.tar.gz': 'abea62dca77ca4645463415bec219a42554146cc0eefd480c760222e423c7db3'}, + {'MDStress-20191228_use_external_voro++_and_EB_lapack.patch': + '566c181f9a6784c81b04226d360ed71d96f99310a231a88919e7fac37e515e92'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Voro++', '0.4.6'), + ('Python', '3.11.3'), +] + +sanity_check_paths = { + 'files': ['bin/tensortools', 'include/mdstress/mds_basicops.h', 'lib/libmdstress.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'PYTHONPATH': 'bin', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch new file mode 100644 index 00000000000..fd2458812bc --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch @@ -0,0 +1,80 @@ +use external EB Voro++ and flexi/openblas as needed + +Åke Sandgren, 2024-11-07 +diff -ru mdstress-library.orig/CMakeLists.txt mdstress-library/CMakeLists.txt +--- mdstress-library.orig/CMakeLists.txt 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/CMakeLists.txt 2024-11-07 11:19:48.125912695 +0100 +@@ -1,4 +1,5 @@ +-cmake_minimum_required(VERSION 2.8) ++cmake_minimum_required(VERSION 3.0) ++project('MDStress') + + enable_language(C) + enable_language(CXX) +@@ -27,42 +28,28 @@ + # COMMAND tar xaf voro++-0.4.6.tar.gz + # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) + #endif() +-FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) +-FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) +-#FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-#FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) ++#FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) ++#FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) ++##FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++##FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) + +-SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H} ${VORO_SOURCES_CC} ${VORO_SOURCES_HH}) ++SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H}) + + INCLUDE_DIRECTORIES(include/mdstress) +-INCLUDE_DIRECTORIES(include/voro++) ++#INCLUDE_DIRECTORIES(include/voro++) + + # attempt to find LAPACK library +-FIND_LIBRARY(LAPACK_LIBRARY_SYS NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-if (NOT LAPACK_LIBRARY_SYS) +- UNSET(LAPACK_LIBRARY_SYS-NOTFOUND) +- UNSET(LAPACK_LIBRARY_SYS) +- # check to see if we need to download LAPACK +- SET(LAPACK_URL http://www.netlib.org/lapack/lapack-3.8.0.tar.gz) +- SET(LAPACK_DOWNLOAD_PATH ${CMAKE_CURRENT_SOURCE_DIR}/contrib/lapack-3.8.0.tar.gz) +- FILE(DOWNLOAD ${LAPACK_URL} ${LAPACK_DOWNLOAD_PATH}) +- EXECUTE_PROCESS( +- COMMAND tar xaf lapack-3.8.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) +- ADD_SUBDIRECTORY(contrib/lapack-3.8.0) +-else() +- FIND_LIBRARY(LAPACK_LIBRARY NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-endif() ++FIND_LIBRARY(LAPACK_LIBRARY NAMES flexiblas openblas lapack liblapack REQUIRED) + + ADD_LIBRARY(mdstress SHARED ${MDSTRESS_SOURCES}) +-TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES}) ++TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES} voro++) + +-INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib/static) ++INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib) + + INSTALL(FILES ${MDSTRESS_SOURCES_H} DESTINATION include/mdstress) +-INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) ++#INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) + + # only process python bindings if requested + if(MDS_BOOSTPYTHON) +diff -ru mdstress-library.orig/src/mds_stressgrid.cpp mdstress-library/src/mds_stressgrid.cpp +--- mdstress-library.orig/src/mds_stressgrid.cpp 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/src/mds_stressgrid.cpp 2024-11-07 09:08:35.761694010 +0100 +@@ -21,7 +21,7 @@ + =========================================================================*/ + + #include "mds_stressgrid.h" +-#include "voro++.hh" ++#include "voro++/voro++.hh" + + using namespace mds; + From e8179601d2e5f4456078d402838affec64a48987 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 7 Nov 2024 15:01:57 +0100 Subject: [PATCH 428/524] adding easyconfigs: jupyterlmod-5.2.1-GCCcore-13.2.0.eb --- .../jupyterlmod-5.2.1-GCCcore-13.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2f0f8aabd7f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '5.2.1' + +# This easyconfig installs the notebook and lab extension of Jupyter Lmod + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows users to interact with +environment modules before launching kernels. The extension uses Lmod's Python +interface to accomplish module-related tasks like loading, unloading, saving +collections, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('JupyterNotebook', '7.2.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['6f9c94d80b813792a6b63aeff5f2672f7d485ce43a7fd5bb7f6fce1c0907cad5'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' From ff06f52024795b19314c8670cff40579b8a1d59e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 7 Nov 2024 15:11:32 +0100 Subject: [PATCH 429/524] add jupyterlmod v5.2.1 to Jupyter-bundle v20240522 --- .../j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb index d6ac6ce1ad0..e58d22ce229 100644 --- a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('JupyterNotebook', '7.2.0'), ('nbclassic', '1.0.0'), ('jupyter-server-proxy', '4.1.2'), - # ('jupyterlmod', '5.0.0'), -- not ready yet, waiting for https://github.com/cmd-ntrf/jupyter-lmod/pull/70 + ('jupyterlmod', '5.2.1'), ('jupyter-resource-usage', '1.0.2'), ] From 340a88a63c48d8899e716591f1a5b58263424201 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 7 Nov 2024 17:07:22 +0100 Subject: [PATCH 430/524] adding easyconfigs: tbl2asn-20230713-GCCcore-13.3.0.eb --- .../tbl2asn-20230713-GCCcore-13.3.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dac64a70d42 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb @@ -0,0 +1,64 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +builddependencies = [ + ('binutils', '2.42'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.41', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['884d706364b81abdd17bee9686d8ff2ae7431c5a14651047c68adf8b31fd8945'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' From c7938df85599d8b059884296fad0c2a2fbe52828 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Nov 2024 17:35:46 +0100 Subject: [PATCH 431/524] add patch to fix vectorization bug in scipy 1.11.1 also to SciPy-bundle 2023.07 w/ iimkl/2023a --- .../s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 25fa6ff36f7..09154f9d830 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -79,6 +79,7 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.11.1_vectorization_error.patch', 'scipy-1.11.1_disable-tests-iimkl.patch', 'scipy-1.11.1_relaxed_test_accuracy.patch', ], @@ -87,6 +88,8 @@ exts_list = [ {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.11.1_vectorization_error.patch': + 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, {'scipy-1.11.1_disable-tests-iimkl.patch': 'e85cf95d343fa4fd9e0045df3a030209a8d7b32a47d6da64ae1efd7b8ef827e3'}, {'scipy-1.11.1_relaxed_test_accuracy.patch': From 36404a365b6ce03113407ede23549a3031634682 Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Thu, 7 Nov 2024 17:43:11 +0100 Subject: [PATCH 432/524] adding easyconfigs: ORCA-6.0.1-gompi-2023b-avx2.eb --- .../o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb new file mode 100644 index 00000000000..854f0424abb --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] + +# orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz +checksums = ['f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2'] + +moduleclass = 'chem' From a305f965dce92b9b39849be3daa2e632a403454b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Nov 2024 17:48:11 +0100 Subject: [PATCH 433/524] add newer Cython as build dependency to SciPy-bundle 2023.07, required for scipy 1.11.1 --- .../s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 09154f9d830..a41da775912 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), # required by scipy + ('Cython', '3.0.8'), ] dependencies = [ @@ -79,7 +80,6 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', - 'scipy-1.11.1_vectorization_error.patch', 'scipy-1.11.1_disable-tests-iimkl.patch', 'scipy-1.11.1_relaxed_test_accuracy.patch', ], @@ -88,8 +88,6 @@ exts_list = [ {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, - {'scipy-1.11.1_vectorization_error.patch': - 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, {'scipy-1.11.1_disable-tests-iimkl.patch': 'e85cf95d343fa4fd9e0045df3a030209a8d7b32a47d6da64ae1efd7b8ef827e3'}, {'scipy-1.11.1_relaxed_test_accuracy.patch': From d218abefb2a6b0fa5c6a1fc1506ca9cd45bd9643 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Nov 2024 20:53:55 +0100 Subject: [PATCH 434/524] remove unused easyconfig for spaln 3.0.6a, replaced with 3.0.6b --- .../s/spaln/spaln-3.0.6a-GCC-12.3.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb deleted file mode 100644 index 0cdb496871d..00000000000 --- a/easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -# updated: Denis Kristak (INUITS) -# Update: Petr Král (INUITS) -easyblock = 'ConfigureMake' - -name = 'spaln' -version = '3.0.6a' - -homepage = 'https://github.com/ogotoh/spaln' -description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps - and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} -# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; -# see also https://github.com/ogotoh/spaln/issues/56 -toolchainopts = {'optarch': False} - -source_urls = ['https://github.com/ogotoh/spaln/archive/'] -sources = ['ver.%(version)s.tar.gz'] -checksums = ['63c46589374e7c2b9a767ef3170504637cb2a57a05d0090a1a8bc6656cd3f254'] - -dependencies = [ - ('zlib', '1.2.13'), - ('Perl', '5.36.1'), -] - -start_dir = 'src' - -# not a standard `configure` - does not accept standard `--prefix` option -# see https://github.com/ogotoh/spaln/issues/74 -prefix_opt = '--exec_prefix=' - -configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb" - -installopts = 'DESTDIR=%(installdir)s/' - -fix_perl_shebang_for = ['seqdb/*.pl'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], - 'dirs': ['seqdb', 'table'], -} - -sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] -modextrapaths = { - 'PATH': 'seqdb', - 'PERL5LIB': 'seqdb', -} - -moduleclass = 'bio' From 41024df0030287af346cde06acf8407834b0cc94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2024 11:36:06 +0100 Subject: [PATCH 435/524] adding easyconfigs: dill-0.3.8-GCCcore-13.2.0.eb --- .../d/dill/dill-0.3.8-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0cc0fb8820c --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.8' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 704118d88612d9483007db447ddffd6e590bbbfd Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 8 Nov 2024 11:54:42 +0100 Subject: [PATCH 436/524] use version 1.34 for libidn --- .../easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb index dac64a70d42..12b79ddde0f 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb @@ -29,12 +29,12 @@ default_easyblock = 'CmdCp' # checksums. components = [ - ('libidn', '1.41', { + ('libidn', '1.34', { 'easyblock': 'ConfigureMake', 'source_urls': [GNU_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'start_dir': '%(namelower)s-%(version)s', - 'checksums': ['884d706364b81abdd17bee9686d8ff2ae7431c5a14651047c68adf8b31fd8945'], + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], }), (name, version, { 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % From dc00e92dee00ffbb129cf2bf14c7a7155c898e18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2024 12:13:23 +0100 Subject: [PATCH 437/524] add missing hatchling build dependency for epiScanpy 0.4.0 w/ foss/2023a --- .../easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb index 552e826a3a2..45d4f74af79 100644 --- a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb @@ -11,6 +11,10 @@ analysis tool Scanpy (Genome Biology, 2018) [Wolf18].""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From fa3f2c922c5aa8b71e3f886972ec6183200b3c7d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 8 Nov 2024 13:52:29 +0100 Subject: [PATCH 438/524] update naming of mustache --- .../Mustache-1.3.3-foss-2023b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/{mustache-hic/mustache-hic-1.3.3-foss-2023b.eb => Mustache/Mustache-1.3.3-foss-2023b.eb} (98%) diff --git a/easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb similarity index 98% rename from easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb rename to easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb index 2eb0c9676c0..6b70a233ac0 100644 --- a/easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb +++ b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'mustache-hic' +name = 'Mustache' version = '1.3.3' homepage = 'https://github.com/ay-lab/mustache' From 5fd37e0e13441ab51468fa667580871848ed8257 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2024 14:00:45 +0100 Subject: [PATCH 439/524] add custom source URL for Mustache --- easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb index 6b70a233ac0..214d5af84bf 100644 --- a/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb +++ b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb @@ -12,6 +12,7 @@ Computer Vision to detect chromatin loops caused by interaction of DNA segments toolchain = {'name': 'foss', 'version': '2023b'} +source_urls = ['https://pypi.python.org/packages/source/m/mustache_hic'] sources = [{'download_filename': 'mustache_hic-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['fd7cca927e36145bf6e43903a79c3222ecfeeb497c8f57657d7647ec6eee5a6b'] From 648993b683788bad98c6532c49138ad8bf9a206c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 8 Nov 2024 14:00:59 +0100 Subject: [PATCH 440/524] bugfix of `HTSplotter-2.11` --- .../h/HTSplotter/HTSplotter-2.11-foss-2023a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb index 5a631178a6b..75808cd8e7a 100644 --- a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb @@ -50,8 +50,12 @@ exts_list = [ }), (name, version, { 'modulename': 'HTSplotter', - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['6067735d14f15ca2fd35963701a96e39edaf0899742bfa7ccc8f9867a0279346'], + # Fixes the following error. + # `TypeError: rv_generic_interval() missing 1 required positional argument: 'confidence'` + # see https://github.com/KatherLab/marugoto/issues/14 + # see also scipy release notes https://docs.scipy.org/doc/scipy/release/1.9.0-notes.html#deprecated-features + 'preinstallopts': "sed -i 's/alpha/confidence/g' HTSplotter/save_hdf5brfiles.py && ", + 'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'], }), ] From 0ac16f380a049e887e945b31bdbd7509a64a7dcb Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 8 Nov 2024 15:28:52 +0100 Subject: [PATCH 441/524] adding easyconfigs: DBD-mysql-4.051-GCC-13.3.0.eb, MariaDB-11.7.0-GCC-13.3.0.eb, Judy-1.0.5-GCCcore-13.3.0.eb --- .../d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb | 30 +++++++++ .../j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb | 34 ++++++++++ .../m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb | 65 +++++++++++++++++++ 3 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb new file mode 100644 index 00000000000..f8f26485760 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.051' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['16969bfae7a080384167be3fb1803450fde87f7b0e2682276b3f6469fa147864'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('MariaDB', '11.7.0'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ad7805e7167 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..437ed1edf42 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.7.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.7.0.tar.gz': 'b0059a9550bb277790f1ec51e0eb329a8fbb8acfd98b5adb259bc0560ff70553'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.5'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.12.7'), # needed by Connect XML + ('Boost', '1.85.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 36cdeed114491b10eec90c8e6f40cc1bb02bb0d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 8 Nov 2024 16:13:57 +0100 Subject: [PATCH 442/524] withelist JuliaPackage from test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 74f98af5cf8..c44a70cce8b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1210,12 +1210,12 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle, + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle & JuliaPackage, PerlBundle, # PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', - 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', - 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] + 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'JuliaPackage', + 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, From d6a2e48763ba3577cc0e89112a429094bd28e8fa Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 9 Nov 2024 12:08:21 +0100 Subject: [PATCH 443/524] test examples from installed version of LightGBM --- .../l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb | 2 +- easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb index 79b61c8d87b..638330e8866 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb @@ -28,7 +28,7 @@ dependencies = [ use_pip = True # example files are not distributed with the sources -_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" _test_cmds_pre = " && ".join([ "mkdir regression", "wget -P regression %s/regression/regression.test" % _test_repo_url, diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb index fdbf6f54f1d..b6a03faf9ca 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ use_pip = True # example files are not distributed with the sources -_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" _test_cmds_pre = " && ".join([ "mkdir regression", "wget -P regression %s/regression/regression.test" % _test_repo_url, From 27965a2d8e3824c3f14c9282ec2e6320d44a5901 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 11 Nov 2024 10:46:04 +0100 Subject: [PATCH 444/524] add Sniffles and necessary deps --- .../p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb | 33 +++++++++++++++++ .../s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb | 37 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..2920aeda78e --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6'] + +builddependencies = [ + ('Cython', '3.0.10') +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ncurses', '6.5'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb new file mode 100644 index 00000000000..394a3863539 --- /dev/null +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Sniffles' +version = '2.0.7' + +homepage = 'https://github.com/fritzsedlazeck/Sniffles' +description = """A fast structural variant caller for long-read sequencing, + Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Pysam', '0.22.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sniffles'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from sniffles import sv'", + "sniffles --help", +] + +moduleclass = 'bio' From f62e1d18451322f19af0668c906074867b83d1f5 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 11 Nov 2024 11:16:45 +0100 Subject: [PATCH 445/524] correct version and add new dep --- .../e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb | 33 +++++++++++++++++++ .../s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb | 5 +-- 2 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb new file mode 100644 index 00000000000..1630a181fbc --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'edlib' +version = '1.3.9.post1' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cogapp', '3.4.1', { + 'checksums': ['a806d5db9e318a1a2d3fce988008179168e7db13e5e55b19b79763f9bb9d2982'], + }), + (name, version, { + # 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], + # 'source_tmpl': '%(version)s.tar.gz', + # fixes `edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory` + # see https://github.com/Martinsos/edlib/issues/217#issuecomment-1736234091 + # 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', + 'checksums': ['b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb index 394a3863539..ad8e962950a 100644 --- a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Sniffles' -version = '2.0.7' +version = '2.4' homepage = 'https://github.com/fritzsedlazeck/Sniffles' description = """A fast structural variant caller for long-read sequencing, @@ -12,6 +12,7 @@ toolchain = {'name': 'GCC', 'version': '13.3.0'} dependencies = [ ('Python', '3.12.3'), ('Pysam', '0.22.1'), + ('edlib', '1.3.9.post1'), ] use_pip = True @@ -20,7 +21,7 @@ sanity_pip_check = True exts_list = [ (name, version, { 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + 'checksums': ['e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4'], }), ] From e7757ee7ccce2af45a30680c1f86f237dd2ff877 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:58:08 +0000 Subject: [PATCH 446/524] adding easyconfigs: Greenlet-3.1.1-GCCcore-13.3.0.eb --- .../Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b54b7ecfcc3 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '3.1.1' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ce3ac6cdb6adf7946475d7ef31777c26d94bccc377e070a7986bd2d5c515467'] + +moduleclass = 'devel' From 43cd0efbd7737b0d363ab9a1405a79a7301f73ad Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:58:49 +0000 Subject: [PATCH 447/524] adding easyconfigs: SQLAlchemy-2.0.36-GCCcore-13.3.0.eb --- .../SQLAlchemy-2.0.36-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..293b3bf2452 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.36' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Greenlet', '3.1.1'), + ('psycopg', '3.2.3'), # optional, postgresql extra + ('Mako', '1.3.5'), # needed by alembic +] + +use_pip = True + +exts_list = [ + ('async-timeout', '5.0.1', { + 'sources': ['async_timeout-%(version)s.tar.gz'], + 'checksums': ['d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3'], + }), + ('asyncpg', '0.30.0', { + 'checksums': ['c551e9928ab6707602f44811817f82ba3c446e018bfe1d3abecc8ba5f3eac851'], + }), + ('sqlalchemy', version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['7f2767680b6d2398aea7082e45a774b2b0767b5c8d8ffb9c8b683088ea9b29c5'], + }), + ('alembic', '1.14.0', { + 'checksums': ['b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1c3a748bdd64175839fcc5ac0acf4d63aba76b7d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:59:37 +0000 Subject: [PATCH 448/524] adding easyconfigs: psycopg-3.2.3-GCCcore-13.3.0.eb --- .../p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..28b9128ff66 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psycopg' +version = '3.2.3' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5764f67c27bec8bfac85764d23c534af2c27b893550377e37ce59c12aac47a2'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PostgreSQL', '16.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From deaa03540ae965a2ca865186507898fba16b71db Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:02:05 +0000 Subject: [PATCH 449/524] adding easyconfigs: scikit-learn-1.5.2-gfbf-2024a.eb --- .../scikit-learn-1.5.2-gfbf-2024a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb new file mode 100644 index 00000000000..aba5adaf848 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.5.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + # Build requires "Cython>=3.0.8" + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'sources': ['scikit_learn-%(version)s.tar.gz'], + 'checksums': ['b4237ed7b3fdd0a4882792e68ef2545d5baa50aca3bb45aa7df468138ad8f94d'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 18cf679f8a480937c6beeb5a7a94340b9ad91da7 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:08:49 +0000 Subject: [PATCH 450/524] added cython builddep --- .../s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb index aba5adaf848..9c2ba9c310f 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -11,11 +11,13 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'gfbf', 'version': '2024a'} +builddependencies = [ + ('Cython', '3.0.10'), +] + dependencies = [ ('Python', '3.12.3'), ('Python-bundle-PyPI', '2024.06'), - # Build requires "Cython>=3.0.8" - # Cython included with Python-bundle-PyPI (0.29.35) is too old ('SciPy-bundle', '2024.05'), ] From 82b2bc31ed777ad75b669183e8f513d13955acdb Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:19:41 +0000 Subject: [PATCH 451/524] added mesonpy --- .../easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb index 9c2ba9c310f..be9c3fd844c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2024a'} builddependencies = [ ('Cython', '3.0.10'), + ('meson-python', '0.16.0'), ] dependencies = [ From 1df0fa8e74def46713e4ff0857d8565876bd5132 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 11 Nov 2024 11:54:46 +0000 Subject: [PATCH 452/524] adding easyconfigs: rapidNJ-2.3.3-GCCcore-12.3.0.eb --- .../r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5a6e44436d9 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' From 1f53f29e706015d48cb7051ce1e48ea01c23ed4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 12 Nov 2024 14:47:51 +0100 Subject: [PATCH 453/524] bump to 2024.4 --- .../g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb index ebc1ba1601a..d93065bbed6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb @@ -15,7 +15,7 @@ # License:: MIT/GPL name = 'GROMACS' -version = '2024.3' +version = '2024.4' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://www.gromacs.org' @@ -42,7 +42,7 @@ patches = [ 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', ] checksums = [ - {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': From 223f2c1b9e7599599bfb406d4510ea237098b057 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Tue, 12 Nov 2024 19:09:01 +0100 Subject: [PATCH 454/524] adding easyconfigs: VTune-2025.0.0.eb --- .../easyconfigs/v/VTune/VTune-2025.0.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb new file mode 100644 index 00000000000..1be37c7d69e --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb @@ -0,0 +1,24 @@ +name = 'VTune' +version = '2025.0.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/e7797b12-ce87-4df0-aa09-df4a272fc5d9/'] +sources = ['intel-vtune-%(version)s.1130_offline.sh'] +checksums = ['6742e5c6b1cd6e4efb794bde5d995ba738be1a991ac84678e0efca04fc080074'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' From dcd7be3f781dda9ac582124e4a9f444f0724f0a0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:13:01 +0100 Subject: [PATCH 455/524] adding easyconfigs: rclone-1.68.1.eb --- .../easyconfigs/r/rclone/rclone-1.68.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb new file mode 100644 index 00000000000..12c72ff4ab8 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.68.1' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['26259526855a12499d00e3a3135ee95e7aeb3ecf2f85886d8c837a2e7b236226'] + +builddependencies = [('Go', '1.22.1', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 0d1c1ff4772169260adca47a4e9e0c6752f556ce Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:30:44 +0100 Subject: [PATCH 456/524] adding easyconfigs: ORCA-6.0.1-gompi-2023a-avx2.eb --- .../o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..bc34fff4fe8 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] + +moduleclass = 'chem' From 5d01bc54db00977ba3019b8e217ba5908042b30e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:42:09 +0100 Subject: [PATCH 457/524] revert format change of checksums in ORCA-6.0.1-gompi-2023b-avx2.eb --- .../easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb index 854f0424abb..6194413a4f1 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb @@ -16,8 +16,9 @@ toolchain = {'name': 'gompi', 'version': '2023b'} download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" # mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] - -# orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz -checksums = ['f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2'] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] moduleclass = 'chem' From d4a8224ef3654a709f0ce9cd0541797d6e1d992f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 10:44:24 +0100 Subject: [PATCH 458/524] fix name for easyconfig file for GROMACS 2024.4 --- ...3b-CUDA-12.4.0.eb => GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb => GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb} (100%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb From 754b3141f1ed8be2fd8397aecbe832b644e6b6eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 10:58:11 +0100 Subject: [PATCH 459/524] add missing hatchling build dependency for scArches 0.6.1 w/ foss/2023a --- .../s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb | 4 ++++ easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb index cb33b614f6f..bcabab4cc73 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -10,6 +10,10 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb index bdcb1ab880c..e6b6f8d4e59 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From 345ea907f238d887390bcd0268d0a8be5a5e52bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 11:58:11 +0100 Subject: [PATCH 460/524] adding easyconfigs: GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb --- ...4.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..7a3c8faccba --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb @@ -0,0 +1,97 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From c8fdb0fb74ed55979ecce8a2143eb2f0fa7f0885 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 13 Nov 2024 14:43:48 +0100 Subject: [PATCH 461/524] [gomkl/2023b] DFT-D4 multicharge wannier90 libxc-nofhc --- .../d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb | 41 ++++++++++++++ easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 +++++++ .../l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb | 53 +++++++++++++++++++ .../multicharge-0.3.0-gomkl-2023b.eb | 39 ++++++++++++++ .../Wannier90/Wannier90-3.1.0-gomkl-2023b.eb | 35 ++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb new file mode 100644 index 00000000000..a59c07c17dc --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'DFT-D4' +version = '3.7.0' + +homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['DFT-D4-3.2.0-remove_module_id.patch'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cffi', '1.15.1'), + ('mstore', '0.3.0'), + ('mctc-lib', '0.3.1'), + ('multicharge', '0.3.0'), +] + +configopts = '-Dpython=true -Dapi_v2=true ' +# if not intel compiler used, lapack mkl is not found. +configopts += '-Dlapack=mkl ' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.mod'], + 'dirs': [], +} + +sanity_check_commands = ["dftd4 --version"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb new file mode 100644 index 00000000000..d5b856a6fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '13.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.6', '', local_comp), + ('imkl', '2023.2.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb new file mode 100644 index 00000000000..709703f2949 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' +versionsuffix = '-nofhc' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# Disable fhc, this needs to support codes (like VASP) relying on the projector augmented wave (PAW) approach +local_common_configopts += ' -DDISABLE_FHC=ON' + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb new file mode 100644 index 00000000000..298e08395e3 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb new file mode 100644 index 00000000000..e1bedb6ba07 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From a316bc83f3482518ad6259d159593ef24372f709 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Nov 2024 15:05:45 +0100 Subject: [PATCH 462/524] Remove bokeh, because it's already merged --- .../b/bokeh/bokeh-3.6.0-gfbf-2024a.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb deleted file mode 100644 index fbdb34a71b6..00000000000 --- a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '3.6.0' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'gfbf', 'version': '2024a'} - -builddependencies = [ - ('meson-python', '0.16.0'), -] - -dependencies = [ - ('Python', '3.12.3'), - ('Python-bundle-PyPI', '2024.06'), - ('SciPy-bundle', '2024.05'), - ('matplotlib', '3.9.2'), - ('PyYAML', '6.0.2'), - ('Pillow-SIMD', '10.4.0'), - ('tornado', '6.4.1'), -] - -use_pip = True - -exts_list = [ - ('xyzservices', '2024.4.0', { - 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], - }), - (name, version, { - 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, - 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["bokeh --help"] - -sanity_pip_check = True - -moduleclass = 'tools' From 9bd5bb154ee97c686e5eaa054f941c8f8e49803f Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 13 Nov 2024 15:14:47 +0100 Subject: [PATCH 463/524] update cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb add sbsa checksum --- .../easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb index a6cbe9ef7e7..76340a4e654 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb @@ -16,7 +16,12 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d'] +checksums = [{ + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '494b640a69feb40ce806a726aa63a1de6b2ec459acbe6a116ef6fe3e6b27877d', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d', +}] dependencies = [('CUDA', '12.6.0')] From 0753acb96039f9096c697ef2ecd7f245293564f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 15:34:21 +0100 Subject: [PATCH 464/524] adding easyconfigs: GROMACS-2024.4-foss-2023b.eb --- .../g/GROMACS/GROMACS-2024.4-foss-2023b.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb new file mode 100644 index 00000000000..778af16ba08 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb @@ -0,0 +1,89 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 3976ba038ec6081e2f06b2ec2f7773fb1810eb57 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Nov 2024 16:01:24 +0100 Subject: [PATCH 465/524] Remove tornado, because it's already merged --- .../t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb deleted file mode 100644 index d4266c8c1c9..00000000000 --- a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "PythonPackage" - -name = "tornado" -version = "6.4.1" - -homepage = "https://github.com/tornadoweb/tornado" -description = "Tornado is a Python web framework and asynchronous networking library." - -toolchain = {"name": "GCCcore", "version": "13.3.0"} - -sources = [SOURCE_TAR_GZ] -patches = ['tornado-6.1_increase-default-timeouts.patch'] -checksums = [ - {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, - {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, -] - -builddependencies = [ - ("binutils", "2.42"), -] -dependencies = [ - ("Python", "3.12.3"), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = "lib" From e389efbfd4760141acc8910b8eeb9777d62eae9d Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 13 Nov 2024 16:35:44 +0100 Subject: [PATCH 466/524] Update easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb index 990ec0677d4..f691f95e191 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb @@ -34,7 +34,7 @@ files_to_copy = [ ] # 7z requires 7z.so plugin in same directory sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], 'dirs': ['libexec/Codecs'], } From 663e776c639e64216155230db594a24df2047c6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 18:35:36 +0100 Subject: [PATCH 467/524] fix long line in easyconfig for GROMACS 2024.4 w/ CUDA 12.4.0 + PLUMED 2.9.2 --- .../GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb index 7a3c8faccba..1fc7764f5a7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb @@ -85,7 +85,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.2', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], }), ] From 419397286785ee360048ffac175c5283a8b70ca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 19:39:38 +0100 Subject: [PATCH 468/524] adding easyconfigs: GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb --- .../GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..5920405282c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb @@ -0,0 +1,97 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 7ee1b3bf760307573be48e9a99793a5473199c97 Mon Sep 17 00:00:00 2001 From: satishk Date: Thu, 14 Nov 2024 10:55:28 +0100 Subject: [PATCH 469/524] adding easyconfigs: Valgrind-3.24.0-gompi-2024a.eb --- .../v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb new file mode 100644 index 00000000000..2c2922383b6 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.24.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['71aee202bdef1ae73898ccf7e9c315134fa7db6c246063afc503aef702ec03bd'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +sanity_check_commands = [ + 'callgrind_annotate --version 2>&1 | grep "%(version)s"', + 'cg_annotate --help', + 'ms_print --version 2>&1 | grep "%(version)s"', + 'valgrind --help', + 'vgdb --help', +] + +moduleclass = 'debugger' From 8831dd2891bd4b15b7ea2d91ead3724e146a046e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 13:20:55 +0100 Subject: [PATCH 470/524] add checksum for dft-d4 --- easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb index a59c07c17dc..02f10d2d9dc 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'gomkl', 'version': '2023b'} source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] patches = ['DFT-D4-3.2.0-remove_module_id.patch'] +checksums = [ + {'v3.7.0.tar.gz': 'f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'}, + {'DFT-D4-3.2.0-remove_module_id.patch': '8c3c81338cb57972580e4cf3db307aa2e44b8b3f6d1ba7ae24fa9d807490a93b'}, +] builddependencies = [ ('CMake', '3.27.6'), From da5266453dd983cc1f1edb250bd1df421bdf8fa0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 14 Nov 2024 19:23:52 +0100 Subject: [PATCH 471/524] adding easyconfigs: trusTEr-0.1.1-20241025-foss-2023a.eb, subset-bam-1.1.0.eb, bamtofastq-1.4.1-GCCcore-12.3.0.eb, TEtranscripts-2.2.3-foss-2023a.eb --- .../bamtofastq-1.4.1-GCCcore-12.3.0.eb | 220 ++++++++++++++++++ .../s/subset-bam/subset-bam-1.1.0.eb | 24 ++ .../TEtranscripts-2.2.3-foss-2023a.eb | 42 ++++ .../trusTEr-0.1.1-20241025-foss-2023a.eb | 36 +++ 4 files changed, 322 insertions(+) create mode 100644 easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb create mode 100644 easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8759374058b --- /dev/null +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,220 @@ +easyblock = 'Cargo' + +name = 'bamtofastq' +version = '1.4.1' + +homepage = 'https://github.com/10XGenomics/bamtofastq' +description = """Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [('bzip2', '1.0.8')] + +crates = [ + ('addr2line', '0.17.0'), + ('adler', '1.0.2'), + ('aho-corasick', '0.7.18'), + ('anyhow', '1.0.53'), + ('autocfg', '1.0.1'), + ('backtrace', '0.3.63'), + ('bincode', '1.3.3'), + ('bio-types', '0.12.0'), + ('bitflags', '1.3.2'), + ('bstr', '0.2.17'), + ('byteorder', '1.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.71'), + ('cfg-if', '1.0.0'), + ('cmake', '0.1.45'), + ('crc32fast', '1.2.1'), + ('crossbeam-channel', '0.5.1'), + ('crossbeam-utils', '0.8.5'), + ('csv', '1.1.6'), + ('csv-core', '0.1.10'), + ('curl-sys', '0.4.49+curl-7.79.1'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('docopt', '1.1.1'), + ('either', '1.6.1'), + ('fastrand', '1.7.0'), + ('flate2', '1.0.22'), + ('form_urlencoded', '1.0.1'), + ('fs-utils', '1.1.4'), + ('gimli', '0.26.0'), + ('glob', '0.3.0'), + ('heck', '0.3.3'), + ('hts-sys', '2.0.2'), + ('idna', '0.2.3'), + ('ieee754', '0.2.6'), + ('instant', '0.1.12'), + ('itertools', '0.10.3'), + ('itoa', '0.4.8'), + ('jobserver', '0.1.24'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.103'), + ('libdeflate-sys', '0.5.0'), + ('libz-sys', '1.1.3'), + ('linear-map', '1.2.0'), + ('log', '0.4.14'), + ('lz4', '1.23.2'), + ('lz4-sys', '1.9.2'), + ('lzma-sys', '0.1.17'), + ('matches', '0.1.9'), + ('memchr', '2.4.1'), + ('min-max-heap', '1.3.0'), + ('miniz_oxide', '0.4.4'), + ('newtype_derive', '0.1.6'), + ('object', '0.27.1'), + ('openssl-src', '111.16.0+1.1.1l'), + ('openssl-sys', '0.9.67'), + ('percent-encoding', '2.1.0'), + ('pkg-config', '0.3.20'), + ('proc-macro2', '1.0.29'), + ('quick-error', '1.2.3'), + ('quote', '1.0.10'), + ('redox_syscall', '0.2.10'), + ('regex', '1.5.4'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.25'), + ('remove_dir_all', '0.5.3'), + ('rust-htslib', '0.38.2'), + ('rustc-demangle', '0.1.21'), + ('rustc_version', '0.1.7'), + ('ryu', '1.0.5'), + ('semver', '0.1.20'), + ('serde', '1.0.135'), + ('serde_bytes', '0.11.5'), + ('serde_derive', '1.0.135'), + ('shardio', '0.8.2'), + ('strsim', '0.10.0'), + ('strum_macros', '0.20.1'), + ('syn', '1.0.80'), + ('tempfile', '3.3.0'), + ('thiserror', '1.0.29'), + ('thiserror-impl', '1.0.29'), + ('tinyvec', '1.5.0'), + ('tinyvec_macros', '0.1.0'), + ('unicode-bidi', '0.3.7'), + ('unicode-normalization', '0.1.19'), + ('unicode-segmentation', '1.8.0'), + ('unicode-xid', '0.2.2'), + ('url', '2.2.2'), + ('vcpkg', '0.2.15'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +checksums = [ + {'bamtofastq-1.4.1.tar.gz': 'cebf968b0eff8911df65102e2be5884e6cd7312f1cb0aba6718bfc2d9407d543'}, + {'addr2line-0.17.0.tar.gz': 'b9ecd88a8c8378ca913a680cd98f0f13ac67383d35993f86c90a70e3f137816b'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-0.7.18.tar.gz': '1e37cfd5e7657ada45f742d6e99ca5788580b5c529dc78faf11ece6dc702656f'}, + {'anyhow-1.0.53.tar.gz': '94a45b455c14666b85fc40a019e8ab9eb75e3a124e05494f5397122bc9eb06e0'}, + {'autocfg-1.0.1.tar.gz': 'cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a'}, + {'backtrace-0.3.63.tar.gz': '321629d8ba6513061f26707241fa9bc89524ff1cd7a915a97ef0c62c666ce1b6'}, + {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'}, + {'bio-types-0.12.0.tar.gz': 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{'pkg-config-0.3.20.tar.gz': '7c9b1041b4387893b91ee6746cddfc28516aff326a3519fb2adf820932c5e6cb'}, + {'proc-macro2-1.0.29.tar.gz': 'b9f5105d4fdaab20335ca9565e106a5d9b82b6219b5ba735731124ac6711d23d'}, + {'quick-error-1.2.3.tar.gz': 'a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0'}, + {'quote-1.0.10.tar.gz': '38bc8cc6a5f2e3655e0899c1b848643b2562f853f114bfec7be120678e3ace05'}, + {'redox_syscall-0.2.10.tar.gz': '8383f39639269cde97d255a32bdb68c047337295414940c68bdd30c2e13203ff'}, + {'regex-1.5.4.tar.gz': 'd07a8629359eb56f1e2fb1652bb04212c072a87ba68546a04065d525673ac461'}, + {'regex-automata-0.1.10.tar.gz': '6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132'}, + {'regex-syntax-0.6.25.tar.gz': 'f497285884f3fcff424ffc933e56d7cbca511def0c9831a7f9b5f6153e3cc89b'}, + {'remove_dir_all-0.5.3.tar.gz': '3acd125665422973a33ac9d3dd2df85edad0f4ae9b00dafb1a05e43a9f5ef8e7'}, + {'rust-htslib-0.38.2.tar.gz': '2aca6626496389f6e015e25433b85e2895ad3644b44de91167d847bf2d8c1a1c'}, + {'rustc-demangle-0.1.21.tar.gz': '7ef03e0a2b150c7a90d01faf6254c9c48a41e95fb2a8c2ac1c6f0d2b9aefc342'}, + {'rustc_version-0.1.7.tar.gz': 'c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084'}, + {'ryu-1.0.5.tar.gz': '71d301d4193d031abdd79ff7e3dd721168a9572ef3fe51a1517aba235bd8f86e'}, + {'semver-0.1.20.tar.gz': 'd4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac'}, + {'serde-1.0.135.tar.gz': '2cf9235533494ea2ddcdb794665461814781c53f19d87b76e571a1c35acbad2b'}, + {'serde_bytes-0.11.5.tar.gz': '16ae07dd2f88a366f15bd0632ba725227018c69a1c8550a927324f8eb8368bb9'}, + {'serde_derive-1.0.135.tar.gz': '8dcde03d87d4c973c04be249e7d8f0b35db1c848c487bd43032808e59dd8328d'}, + {'shardio-0.8.2.tar.gz': '669590a22936d55698744e4096bc46fc8f935f492fe86b2f09cbdbb6d937b65a'}, + {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'}, + {'strum_macros-0.20.1.tar.gz': 'ee8bc6b87a5112aeeab1f4a9f7ab634fe6cbefc4850006df31267f4cfb9e3149'}, + {'syn-1.0.80.tar.gz': 'd010a1623fbd906d51d650a9916aaefc05ffa0e4053ff7fe601167f3e715d194'}, + {'tempfile-3.3.0.tar.gz': '5cdb1ef4eaeeaddc8fbd371e5017057064af0911902ef36b39801f67cc6d79e4'}, + {'thiserror-1.0.29.tar.gz': '602eca064b2d83369e2b2f34b09c70b605402801927c65c11071ac911d299b88'}, + {'thiserror-impl-1.0.29.tar.gz': 'bad553cc2c78e8de258400763a647e80e6d1b31ee237275d756f6836d204494c'}, + {'tinyvec-1.5.0.tar.gz': 'f83b2a3d4d9091d0abd7eba4dc2710b1718583bd4d8992e2190720ea38f391f7'}, + {'tinyvec_macros-0.1.0.tar.gz': 'cda74da7e1a664f795bb1f8a87ec406fb89a02522cf6e50620d016add6dbbf5c'}, + {'unicode-bidi-0.3.7.tar.gz': '1a01404663e3db436ed2746d9fefef640d868edae3cceb81c3b8d5732fda678f'}, + {'unicode-normalization-0.1.19.tar.gz': 'd54590932941a9e9266f0832deed84ebe1bf2e4c9e4a3554d393d18f5e854bf9'}, + {'unicode-segmentation-1.8.0.tar.gz': '8895849a949e7845e06bd6dc1aa51731a103c42707010a5b591c0038fb73385b'}, + {'unicode-xid-0.2.2.tar.gz': '8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3'}, + {'url-2.2.2.tar.gz': 'a507c383b2d33b5fc35d1861e77e6b383d158b2da5e14fe51b83dfedf6fd578c'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb new file mode 100644 index 00000000000..f9e6778cec2 --- /dev/null +++ b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'subset-bam' +version = '1.1.0' + +homepage = 'https://github.com/10XGenomics/subset-bam' +description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, +most commonly the cell barcode tag.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/10XGenomics/subset-bam/releases/download/v%(version)s/'] + +sources = [{'download_filename': 'subset-bam_linux', 'filename': name}] +checksums = ['05496ea56d52becdb7972528af0a486be1d52c1749e35bea9ae4c41215ed0a1b'] + +sanity_check_paths = { + 'dirs': [], + 'files': [name], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb new file mode 100644 index 00000000000..ab7aa3071a8 --- /dev/null +++ b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TEtranscripts' +version = '2.2.3' + +homepage = 'https://github.com/mhammell-laboratory/TEtranscripts' +description = """TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads +to both genes & transposable elements. +TEtranscripts then performs differential analysis using DESeq2.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['e53577e8e73e41c6495fb819977e3e537bbeac7b2fa1635029201a37ee0bf7b8'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pysam', '0.22.0'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'TEToolkit'} + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/TEtranscripts', 'bin/TEcount'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'TEtranscripts --version', + 'TEcount --version', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb new file mode 100644 index 00000000000..7cc222efe16 --- /dev/null +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'trusTEr' +version = '0.1.1-20241025' +local_commit = '6358eef' + +homepage = 'https://github.com/raquelgarza/truster' +description = """Takes fastq files from 10x single cell RNA sequencing, clusters cells using Seurat, +and can be used to produce read count matrices in a cluster level. +You can also quantify reads per cluster having predefined clusters.""" + +source_urls = ['https://github.com/raquelgarza/truster/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef6f454a73f545e5f90a28a80d388afb763a43ac1256f3c182bf947728b4e39a'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CellRanger', '8.0.1', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('Seurat', '5.1.0', '-R-%(rver)s'), + ('STAR', '2.7.11a'), + ('velocyto', '0.17.17'), + ('TEtranscripts','2.2.3'), + ('bamtofastq','1.4.1'), + ('subset-bam', '1.1.0-', '', SYSTEM), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 9d1614cc9c8896507ababec14ab509a666414912 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 20:05:15 +0100 Subject: [PATCH 472/524] put toolchain in a different pr --- easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb deleted file mode 100644 index d5b856a6fe9..00000000000 --- a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Toolchain" - -name = 'gomkl' -version = '2023b' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" - -toolchain = SYSTEM - -local_comp = ('GCC', '13.2.0') - -dependencies = [ - local_comp, - ('OpenMPI', '4.1.6', '', local_comp), - ('imkl', '2023.2.0', '', ('gompi', version)), -] - -moduleclass = 'toolchain' From 07234dfa0d4766a6f9743b1612d04b533a4582b3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 20:07:37 +0100 Subject: [PATCH 473/524] {toolchain}[gomkl-2023b] gomkl/2023b --- easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb new file mode 100644 index 00000000000..d5b856a6fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '13.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.6', '', local_comp), + ('imkl', '2023.2.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' From fb7ffabc5dc8fe3264a0f8f2fd31d1999924fdd3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 21:05:11 +0100 Subject: [PATCH 474/524] add imkl --- .../i/imkl/imkl-2023.2.0-gompi-2023b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb new file mode 100644 index 00000000000..e194f389253 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/adb8a02c-4ee7-4882-97d6-a524150da358/'] +sources = ['l_onemkl_p_%(version)s.49497_offline.sh'] +checksums = ['4a0d93da85a94d92e0ad35dc0fc3b3ab7f040bd55ad374c4d5ec81a57a2b872b'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' From 69034cbc04e07aa1cd3cc8945bb5b8474de1d7d5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 15 Nov 2024 11:33:14 +0100 Subject: [PATCH 475/524] truster ec - fix whitespace --- .../t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb index 7cc222efe16..9c26af4b15c 100644 --- a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -24,8 +24,8 @@ dependencies = [ ('Seurat', '5.1.0', '-R-%(rver)s'), ('STAR', '2.7.11a'), ('velocyto', '0.17.17'), - ('TEtranscripts','2.2.3'), - ('bamtofastq','1.4.1'), + ('TEtranscripts', '2.2.3'), + ('bamtofastq', '1.4.1'), ('subset-bam', '1.1.0-', '', SYSTEM), ] From 997fd8a94f3b4678c4b58b6631493ad62a9ea9f3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 15 Nov 2024 11:51:36 +0100 Subject: [PATCH 476/524] Update trusTEr-0.1.1-20241025-foss-2023a.eb - fix typo --- .../easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb index 9c26af4b15c..3bea1107bfc 100644 --- a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ ('velocyto', '0.17.17'), ('TEtranscripts', '2.2.3'), ('bamtofastq', '1.4.1'), - ('subset-bam', '1.1.0-', '', SYSTEM), + ('subset-bam', '1.1.0', '', SYSTEM), ] use_pip = True From e58d753e9b1a905165cdfe0dcefdf00c9a7d6180 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 15 Nov 2024 15:10:11 +0100 Subject: [PATCH 477/524] eccodes --- .../e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb | 46 +++++++++++++++++++ .../l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb | 36 +++++++++++++++ .../libaec/libaec-1.1.3_install_binary.patch | 11 +++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb new file mode 100644 index 00000000000..2aa0915ea2e --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.38.3' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['2f13adc4fbdfa3ea11f75ce4ed8937bf40a8fcedd760a519b15e4e17dedc9424'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('ecBuild', '3.8.5'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libaec', '1.1.3'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..267acc5aa3d --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.1.3' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ["libaec-1.1.3_install_binary.patch"] + +checksums = ['453de44eb6ea2500843a4cf4d2e97d1be251d2df7beae6c2ebe374edcb11e378', + '52fcdeacd9c27108dffafd8109012902fa63fb2e39803670a3ba16f313628f4c'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/graec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['graec --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch new file mode 100644 index 00000000000..29d7f8e0c7b --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch @@ -0,0 +1,11 @@ +# The binary is not installed by default which caused the sanity check to fail +# @author Stefan Wolfsheimer, SURF + +diff -uNr libaec-v1.1.3.orig/src/CMakeLists.txt libaec-v1.1.3/src/CMakeLists.txt +--- libaec-v1.1.3.orig/src/CMakeLists.txt 2024-11-15 14:21:05.177185441 +0100 ++++ libaec-v1.1.3/src/CMakeLists.txt 2024-11-15 14:21:39.702841450 +0100 +@@ -76,3 +76,4 @@ + COMPILE_DEFINITIONS "${libaec_COMPILE_DEFINITIONS}") + + install(TARGETS aec_static aec_shared sz_static sz_shared) ++install(TARGETS graec RUNTIME DESTINATION bin) From 9ae86e469e511278d39658b5c54b28f403b30901 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 15 Nov 2024 15:32:05 +0100 Subject: [PATCH 478/524] add CDO UDUNITS --- .../c/CDO/CDO-2.4.4-gompi-2024a.eb | 57 +++++++++++++++++++ .../UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb | 44 ++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb new file mode 100644 index 00000000000..57b6de8e609 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb @@ -0,0 +1,57 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.4.4' + + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'cstd': 'c++20', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29649/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49f50bd18dacd585e9518cfd4f55548f692426edfb3b27ddcd1c653eab53d063'] + +builddependencies = [ + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('ecCodes', '2.38.3'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.5'), + ('libxml2', '2.12.7'), + ('netCDF', '4.9.2'), + ('PROJ', '9.4.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.40'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..12a51d8afd4 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('expat', '2.6.2')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 2b970e1df3d9f56f30766d5b9e65098437eba11f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 15 Nov 2024 16:48:14 +0000 Subject: [PATCH 479/524] tests added, GMP added correctly --- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb index e4a2c353676..a181d6523c8 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb @@ -31,9 +31,18 @@ builddependencies = [ ('CMake', '3.27.6'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('googletest', '1.14.0'), +] + +dependencies = [ ('GMP', '6.3.0'), ] +preconfigopts = "sed -i 's/c++11/c++14/g' %(builddir)s/raxml-ng/CMakeLists.txt && " +configopts = '-DUSE_GMP=ON ' + +runtest = 'test ' + sanity_check_paths = { 'files': ['bin/raxml-ng'], 'dirs': [], From c993951349521a83803336a4735f671377dcdf61 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sun, 17 Nov 2024 15:46:03 +0100 Subject: [PATCH 480/524] Add netCDF --- .../netCDF-C++4-4.3.1-gompi-2024a.eb | 28 +++++++++ .../netCDF-Fortran-4.6.1-gompi-2024a.eb | 28 +++++++++ .../n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 54 +++++++++++++++++ .../netcdf4-python-1.7.1.post2-foss-2024a.eb | 58 +++++++++++++++++++ ...st2_relax_tolerance_compression_test.patch | 15 +++++ .../p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb | 35 +++++++++++ 6 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..1b9a80b189c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [ + ('netCDF', '4.9.2'), +] + + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb new file mode 100644 index 00000000000..2bc6e207794 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb new file mode 100644 index 00000000000..86160357109 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -0,0 +1,54 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch'] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch': + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('CMake', '3.29.3'), + ('Doxygen', '1.11.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('cURL', '8.7.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.6'), + ('bzip2', '1.0.8'), + ('libxml2', '2.12.7'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb new file mode 100644 index 00000000000..912e23a55b7 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.7.1.post2' + + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = "Python/numpy interface to netCDF." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('netCDF', '4.9.2'), + ('cURL', '8.7.1'), + ('mpi4py', '4.0.1'), +] + +fix_python_shebang_for = ['bin/*'] +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cftime', '1.6.4', { + 'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netcdf4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'}, + {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch': + '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..be4deb77f96 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-1.7.1.post2.orig/test/test_compression_szip.py netcdf4-1.7.1.post2/test/test_compression_szip.py +--- netcdf4-1.7.1.post2.orig/test/test_compression_szip.py 2024-10-07 16:01:21.276893761 +0200 ++++ netcdf4-1.7.1.post2/test/test_compression_szip.py 2024-10-07 16:27:47.424436617 +0200 +@@ -35,7 +35,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb new file mode 100644 index 00000000000..b586cfd0da4 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.13.0' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Perl', '5.38.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = [ + '', + '--enable-shared', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = {'PNETCDF': ''} + +moduleclass = 'data' From a1e39b0d7469ebd98596e5b067eb9584d2979e51 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sun, 17 Nov 2024 17:27:02 +0100 Subject: [PATCH 481/524] Move file to the right folder --- .../{netCDF-C++ => netCDF-C++4}/netCDF-C++4-4.3.1-gompi-2024a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/{netCDF-C++ => netCDF-C++4}/netCDF-C++4-4.3.1-gompi-2024a.eb (100%) diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb similarity index 100% rename from easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb rename to easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb From fdd8fbe49a8a973cccd7977bdc86c10840d58dc5 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 17 Nov 2024 17:46:33 +0100 Subject: [PATCH 482/524] use SHLIB_EXT --- .../easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb index aceab404bda..695a90190e0 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -26,7 +26,7 @@ dependencies = [ configopts = '-DPMT_BUILD_RAPL=1 -DPMT_BUILD_NVML=1 -DPMT_BUILD_NVIDIA=1' sanity_check_paths = { - 'files': ["lib/libpmt.so", "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], + 'files': ["lib/libpmt.%s" % SHLIB_EXT, "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], 'dirs': ["lib", "include"], } From e983a3225e16ec05b5da3829fd859d5a621f6788 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 17 Nov 2024 21:00:35 +0100 Subject: [PATCH 483/524] use SHLIB_EXT --- .../easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb index 1b9a80b189c..909bd06a674 100644 --- a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -21,7 +21,7 @@ dependencies = [ sanity_check_paths = { - 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], 'dirs': [], } From 35786a0873e32877a694ac76179cf872ff7122a5 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Mon, 18 Nov 2024 10:28:09 +0100 Subject: [PATCH 484/524] remove unnecessary comments --- .../easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb index 1630a181fbc..96672c2751b 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb @@ -21,11 +21,6 @@ exts_list = [ 'checksums': ['a806d5db9e318a1a2d3fce988008179168e7db13e5e55b19b79763f9bb9d2982'], }), (name, version, { - # 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], - # 'source_tmpl': '%(version)s.tar.gz', - # fixes `edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory` - # see https://github.com/Martinsos/edlib/issues/217#issuecomment-1736234091 - # 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', 'checksums': ['b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa'], }), ] From f7a10c1213920e079ad3c3d86dde85e37ac1542d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 14:21:03 +0100 Subject: [PATCH 485/524] adding easyconfigs: snpEff-5.2c-GCCcore-12.3.0-Java-11.eb --- .../snpEff-5.2c-GCCcore-12.3.0-Java-11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..c9f29979a1d --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 1185b3243891dd8bfdf0078924c7644ca653e648 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 14:32:06 +0100 Subject: [PATCH 486/524] adding easyconfigs: Lightning-2.2.1-foss-2023a.eb --- .../l/Lightning/Lightning-2.2.1-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb new file mode 100644 index 00000000000..5635e783f7c --- /dev/null +++ b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Lightning' +version = '2.2.1' + +homepage = 'https://github.com/Lightning-AI/pytorch-lightning' +description = """ +The deep learning framework to pretrain, finetune and deploy AI models. +Lightning has 4 core packages: + PyTorch Lightning: Train and deploy PyTorch at scale. + Lightning Fabric: Expert control. + Lightning Data: Blazing fast, distributed streaming of training data from cloud storage. + Lightning Apps: Build AI products and ML workflows. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3e46d596b32cafd1fb9b21fdba1b1767df97b1af5cc702693d1c51df60b19aa'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', version), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From d69a35cc9263e733fb7129b391d01464235f3a33 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 17:18:03 +0100 Subject: [PATCH 487/524] adding easyconfigs: imgaug-0.4.1-foss-2023a.eb --- .../i/imgaug/imgaug-0.4.1-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb new file mode 100644 index 00000000000..2b1f0c837e5 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.1' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pillow', '10.0.0'), + ('matplotlib', '3.7.2'), + ('scikit-image', '0.22.0'), + ('OpenCV', '4.8.1', '-contrib'), + ('Shapely', '2.0.1'), + ('imageio', '2.33.1'), +] + +source_urls = ['https://github.com/nsetzer/imgaug/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['imgaug-0.4.1_openvc_requirement.patch'] +checksums = [ + {'0.4.1.tar.gz': 'dd9655f8d871da35c37cf674ba35c76175a77aeac517e8dafe6673c8f853115f'}, + {'imgaug-0.4.1_openvc_requirement.patch': '0e0993322184c56115ea04262f8eacef4a86a9aa7b26c8cd67258ccaa441d8a7'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From ff9dcb46d48f0ec8a2507956ca67f8dd9e0a541e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 18 Nov 2024 19:30:38 +0100 Subject: [PATCH 488/524] adding easyconfigs: Advisor-2025.0.0.eb, Inspector-2024.2.0.eb --- .../easyconfigs/a/Advisor/Advisor-2025.0.0.eb | 27 +++++++++++++++++++ .../i/Inspector/Inspector-2024.2.0.eb | 19 +++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb new file mode 100644 index 00000000000..1f057b7f100 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb @@ -0,0 +1,27 @@ +name = 'Advisor' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/advisor.html' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/fe95ae4a-3692-4e31-919d-3e7bdf5832f1/'] +sources = ['intel-advisor-%(version)s.798_offline.sh'] +checksums = ['bf85d4b0bd199a2babdff6b4bd3885ce569a3ad0e992b99b2e14dbb30af88cd4'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb new file mode 100644 index 00000000000..0d345bc2c5e --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb @@ -0,0 +1,19 @@ + +name = 'Inspector' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/1549c5b3-cf23-4595-9593-b5d0460a8dcd/'] +sources = ['l_inspector_oneapi_p_%(version)s.22_offline.sh'] +checksums = ['e2aab9b1b428d0c23184beae8caac55fa3d3f973ac51a6b6908eb38b0d9097ed'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 2e8f6f6d75af079b396043f05e2a154a4c81327d Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 18 Nov 2024 16:48:28 -0500 Subject: [PATCH 489/524] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb index 86160357109..95e48775eeb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -48,7 +48,7 @@ configopts = [ ] # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests -pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +pretestopts = "PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe " runtest = 'test' moduleclass = 'data' From f991c85b6845e65063133c9a31c1eb962775b3ef Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 23:59:40 +0100 Subject: [PATCH 490/524] adding easyconfigs: timm-1.0.8-foss-2023a.eb --- .../t/timm/timm-1.0.8-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb new file mode 100644 index 00000000000..a954aa9e443 --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0'), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 5a5f662d3272c63b5523bb87e8c966554e15906e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Nov 2024 00:45:48 +0100 Subject: [PATCH 491/524] use dynamic environment name based on Julia version in RCall v0.13.17 --- .../r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 4da1b0f58aa..bb9b6221bf8 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -222,8 +222,10 @@ exts_list = [ }), ] +local_julia_env = "%(installdir)s/environments/v" + '.'.join(local_juliaver.split('.')[:2]) + sanity_check_commands = [ - """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % local_julia_env, ] sanity_check_paths = { From ac70aacc13cb3bb9ec2b47313c4f9cc351f9f9df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Nov 2024 01:48:43 +0100 Subject: [PATCH 492/524] use dynamic environment name based on Julia version in Circuitscape v5.12.3 --- .../c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index f9909fe5c7a..8e8e7e2f86b 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -403,8 +403,10 @@ exts_list = [ }), ] +_julia_env = "%(installdir)s/environments/v" + '.'.join(_julia_ver.split('.')[:2]) + sanity_check_commands = [ - """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % _julia_env, ] moduleclass = 'lib' From 26dca3a8cff05d2264c881b9d200cf634d10a1db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Tue, 19 Nov 2024 09:31:15 +0100 Subject: [PATCH 493/524] {compiler}[system/system] NVHPC-24.11-CUDA-12.6.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb new file mode 100644 index 00000000000..546b28e7147 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb @@ -0,0 +1,73 @@ +name = 'NVHPC' +version = '24.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2024_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + 'f2f64e5dec5e90dad5e12a31a992172b0aa19abf872ef1c54a1a437c7008eefb', + local_tarball_tmpl % 'x86_64': + '0c27d66ed0e2d3007d30ac904922a9abf96475197dc0f4dcc6316d235a1dc0c3', + } +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.18', '', ('GCCcore', local_gccver)), + ('CUDA', '12.6.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 589c7197cb718d1ec78f20992f5f81a995387d9d Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 19 Nov 2024 10:48:04 +0100 Subject: [PATCH 494/524] adding easyconfigs: absl-py-2.1.0-GCCcore-13.3.0.eb --- .../a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fb76611558b --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From ba767f37bcd4f71579732320a9a9a13c09a2fef4 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Nov 2024 10:32:23 +0000 Subject: [PATCH 495/524] adding easyconfigs: MATLAB-2024b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2024b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb new file mode 100644 index 00000000000..c53c320205f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb @@ -0,0 +1,28 @@ +name = 'MATLAB' +version = '2024b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Linux.iso' % (version)] +checksums = ['4e4499d93b4909b750ee2a6444af107cd5c1c62e75020c3e1625e946c6693573'] + +download_instructions = 'Download %s from mathworks.com' % sources[0] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 0b39d057e1f106c73d595b2572caca2ba2ee0926 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 19 Nov 2024 12:12:29 +0100 Subject: [PATCH 496/524] adding easyconfigs: Spectre-0.2.1-foss-2023a.eb --- .../s/Spectre/Spectre-0.2.1-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb new file mode 100644 index 00000000000..a2a82a58532 --- /dev/null +++ b/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Spectre' +version = '0.2.1' + +homepage = 'https://github.com/fritzsedlazeck/Spectre' +description = """Spectre is a long read copy number variation (CNV) caller. Spectre is designed to detect large CNVs +(>100kb) in a couple of minutes depending on your hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://pypi.org/packages/source/s/spectre-cnv/'] +sources = [{'download_filename': 'spectre_cnv-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a5ab6487bdf239f4df0158632020d57be3cc78831e0fb1f41f27c5a79060cf5a'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = [ + "spectre --help", +] + +moduleclass = 'bio' From 8e62edadb9fc10f348b6cb21ceab0c3813a2efef Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 19 Nov 2024 15:08:09 +0100 Subject: [PATCH 497/524] adding easyconfigs: Bazel-7.4.1-GCCcore-13.3.0.eb --- .../b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1fc72e512e2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +name = 'Bazel' +version = '7.4.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +checksums = ['83386618bc489f4da36266ef2620ec64a526c686cf07041332caff7c953afaf5'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), +] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' From 70b7ff659f79b10b645b8284cc29f9740fb42a9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 21 Nov 2024 15:21:21 +0100 Subject: [PATCH 498/524] patch a segfaulting test for `NECI` --- .../n/NECI/NECI-20230620-foss-2023a.eb | 6 +++++- .../n/NECI/NECI-20230620_segfault.patch | 21 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb index becc50b238e..09dce5c1aab 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -19,7 +19,11 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = [None] +patches = ['NECI-20230620_segfault.patch'] +checksums = [ + None, + 'f0b5f62e115a1e07d6b90bc66ee9957a5f5d686bef65beba9c2be4bd8f29f0e4', +] builddependencies = [ ('CMake', '3.26.3'), diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch new file mode 100644 index 00000000000..0a63b605dd3 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch @@ -0,0 +1,21 @@ +Fixes SEGFAULT error in tests. +See https://github.com/ghb24/NECI_STABLE/issues/18 +Author: Petr Král (INUITS) +--- unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90.orig 2023-06-20 10:15:17.000000000 +0200 ++++ unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90 2024-11-21 14:58:46.602604509 +0100 +@@ -64,6 +64,7 @@ + nmaxy = 2 + nmaxz = 2 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + tOrbECutoff = .false. + + allocate(projedet(nel,1)); projedet(:,1) = [1,2] +@@ -403,6 +404,7 @@ + tOrbECutoff = .false. + niftot = 1 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + + t_back_spawn_flex = .true. + occ_virt_level = 0 From 5dd1cdab1b8c2b952e5d5a7324e81da310124d24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 21 Nov 2024 16:34:58 +0000 Subject: [PATCH 499/524] Fix typo in ParaView copts --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 8f312f89318..340952c3338 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -44,7 +44,7 @@ dependencies = [ _copts = [ # Basic configuration - '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON' + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', '-DPARAVIEW_ENABLE_FFMPEG=ON', From d447d825a3e7448e0b0b11020d4c06ef8386d4f7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 22 Nov 2024 11:13:22 +0100 Subject: [PATCH 500/524] adding easyconfigs: JAGS-4.3.2-foss-2024a.eb --- .../j/JAGS/JAGS-4.3.2-foss-2024a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb new file mode 100644 index 00000000000..1077c8fc2a9 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.2' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download'), +] +sources = [SOURCE_TAR_GZ] +checksums = ['871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["echo 'list modules' | %(namelower)s"] + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 4672cb2d36ad2be1d2270b2b3375d1f69bb3a038 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 11:52:39 +0100 Subject: [PATCH 501/524] adding easyconfigs: Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb --- .../Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b1869b01783 --- /dev/null +++ b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Slurm-Viewer' +version = '1.0.1' + +homepage = 'https://gitlab.com/lkeb/slurm_viewer' +description = """View the status of a Slurm cluster, including nodes and queue.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('pydantic', '2.7.4'), +] + +use_pip = True + +exts_list = [ + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('textual', '0.85.2', { + 'checksums': ['2a416995c49d5381a81d0a6fd23925cb0e3f14b4f239ed05f35fa3c981bb1df2'], + }), + ('textual-plotext', '0.2.1', { + 'source_tmpl': 'textual_plotext-%(version)s.tar.gz', + 'checksums': ['bc6f2d75d8e20dda6321f8254dc3decda8f41f60e6e70a3ddd83b652b890c081'], + }), + ('asyncssh', '2.18.0', { + 'checksums': ['1a322161c01f60b9719dc8f39f80db71e61f3f5e04abbc3420ce503126d87123'], + }), + ('slurm-viewer', version, { + 'source_tmpl': 'slurm_viewer-%(version)s-py3-none-any.whl', + 'checksums': ['2e42662881458701a09770a52062cb065527e30a39aac35165056f4ccf288f52'], + }), +] + +sanity_check_paths = { + 'files': ['bin/slurm-viewer', 'bin/slurm-viewer-init'], + 'dirs': ['lib'] +} + +sanity_pip_check = True + +modloadmsg = """Slurm Viewer requires a configuration file. +You can make a default settings file in your home directory by running slurm-viewer-init, +or you can point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" + +moduleclass = 'tools' From d8f9f592d8e3b7c1eb0c11bac69bca570915c68f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 22 Nov 2024 12:04:26 +0100 Subject: [PATCH 502/524] fix parallel for cppyy-cling and remove unnecessary c++std --- easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb index bcd242d9d23..89c6bc40e3d 100644 --- a/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('cppyy-cling', '6.30.0', { 'modulename': False, - 'preinstallopts': "export STDCXX=14 && ", + 'preinstallopts': 'MAKE_NPROCS=%(parallel)s', 'checksums': ['5d9e0551a4cb618eb3392001b3dc2c6294f02257f02fcd4d868999ba04f92af1'], }), ('cppyy-backend', '1.15.2', { From 76d684b9180d26d522b222d275b6a00c1b77db9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 12:20:19 +0100 Subject: [PATCH 503/524] add build dependency on binutils --- .../s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb index b1869b01783..d7fd824495b 100644 --- a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb @@ -9,6 +9,7 @@ description = """View the status of a Slurm cluster, including nodes and queue." toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ + ('binutils', '2.40'), ('hatchling', '1.18.0'), ('poetry', '1.6.1'), ] From 0ff5111ec219a4be015fb60c04dc80ede12189fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 13:42:47 +0100 Subject: [PATCH 504/524] Rename to SlurmViewer --- ....1-GCCcore-13.2.0.eb => SlurmViewer-1.0.1-GCCcore-13.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/Slurm-Viewer/{Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb => SlurmViewer-1.0.1-GCCcore-13.2.0.eb} (98%) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb similarity index 98% rename from easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb index d7fd824495b..371a8d85eea 100644 --- a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'Slurm-Viewer' +name = 'SlurmViewer' version = '1.0.1' homepage = 'https://gitlab.com/lkeb/slurm_viewer' From e96add3b085d31949a57b9b3a8f45e41ec0d5dcc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 14:11:28 +0100 Subject: [PATCH 505/524] rename directory to SlurmViewer as well --- .../SlurmViewer-1.0.1-GCCcore-13.2.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{Slurm-Viewer => SlurmViewer}/SlurmViewer-1.0.1-GCCcore-13.2.0.eb (100%) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb similarity index 100% rename from easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb From f36cd87a6a5c90f0a1a2388b4e98b5436f3a4c0e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 22 Nov 2024 14:31:48 +0100 Subject: [PATCH 506/524] adding easyconfigs: R2jags-0.8-9-foss-2023a-R-4.3.2.eb --- .../R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..0784b3e87c1 --- /dev/null +++ b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'R2jags' +version = '0.8-9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/R2jags' +description = "Providing wrapper functions to implement Bayesian analysis in JAGS." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['df06b8f919eed8dd65bca29bbe7e337718142734d6a31818ce1e49db8faee14c'] + +dependencies = [ + ('R', '4.3.2'), + ('rjags', '4-15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 16242b712e57b7dde64d5f655e98e3db26540295 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:32:05 +0200 Subject: [PATCH 507/524] {mpi}[NVHPC/24.9] Add OpenMPI 5.0.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb | 63 +++++++++++++++++++ ...MPI-5.0.3_disable_opal_path_nfs_test.patch | 33 ++++++++++ .../OpenMPI-5.0.3_fix_hle_make_errors.patch | 25 ++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb new file mode 100644 index 00000000000..e6c772bf64e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb @@ -0,0 +1,63 @@ +name = 'OpenMPI' +version = '5.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '24.9-CUDA-12.6.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-5.0.3_fix_hle_make_errors.patch', + 'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch', + ('OpenMPI-5.0.2_build-with-internal-cuda-header.patch', 1) +] +checksums = [ + {'openmpi-5.0.3.tar.bz2': + '990582f206b3ab32e938aa31bbf07c639368e4405dca196fabe7f0f76eeda90b'}, + {'OpenMPI-5.0.3_fix_hle_make_errors.patch': + '881c907a9f5901d5d6af41cd33dffdcecba4a67a9e5123e602542aea57a80895'}, + {'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch': + '75d4417e35252ea3a19b2792f1b06e9aeb408c253aa4921d77226d57b71dee45'}, + {'OpenMPI-5.0.2_build-with-internal-cuda-header.patch': + 'f52dc470543f35efef10d651dd159c771ae25f8f76a420d20d87abf4dc769ed7'}, +] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Perl', '5.38.2'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('hwloc', '2.10.0'), + ('libevent', '2.1.12'), + ('UCX', '1.16.0'), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('libfabric', '1.21.0'), + ('PMIx', '5.0.2'), + ('PRRTE', '3.0.5'), + ('UCC', '1.3.0'), + ('UCC-CUDA', '1.3.0', '-CUDA-%(cudaver)s'), +] + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +preconfigopts = 'nvc -Iopal/mca/cuda/include -shared opal/mca/cuda/lib/cuda.c -o opal/mca/cuda/lib/libcuda.so && ' +# Update configure to include changes from the "disable_opal_path_nfs_test" patch +preconfigopts += './autogen.pl --force && ' + +configopts = '--with-cuda=%(start_dir)s/opal/mca/cuda ' +# Required to prevent internal compiler error in opal. +configopts += '--enable-alt-short-float=no ' +# Set PGI compilers manually, as NVHPC compilers are not correctly detected +configopts += 'CC=pgcc CXX=pgc++ FC=pgfortran ' + +# site specific options +# configopts += '--without-psm2 ' +# configopts += '--disable-oshmem ' +# configopts += '--with-gpfs ' +configopts += '--with-slurm ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch new file mode 100644 index 00000000000..09d9f829f06 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch @@ -0,0 +1,33 @@ +Disable opal_path_nfs test in OpenMPI 5.0.3 as this test can easily fail on some systems, +when NFS mounts are used. Generally, this test is flaky, which may prevent users +from installing OpenMPI for no apparent reason. + +diff --git a/test/util/Makefile.am b/test/util/Makefile.am +index e5ad472..33d63c4 100644 +--- a/test/util/Makefile.am ++++ b/test/util/Makefile.am +@@ -38,7 +38,6 @@ AM_CPPFLAGS = -I$(top_srcdir)/test/support + + check_PROGRAMS = \ + opal_bit_ops \ +- opal_path_nfs \ + bipartite_graph \ + opal_sha256 + +@@ -80,11 +79,11 @@ opal_bit_ops_LDADD = \ + $(top_builddir)/test/support/libsupport.a + opal_bit_ops_DEPENDENCIES = $(opal_path_nfs_LDADD) + +-opal_path_nfs_SOURCES = opal_path_nfs.c +-opal_path_nfs_LDADD = \ +- $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ +- $(top_builddir)/test/support/libsupport.a +-opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) ++# opal_path_nfs_SOURCES = opal_path_nfs.c ++# opal_path_nfs_LDADD = \ ++# $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ ++# $(top_builddir)/test/support/libsupport.a ++# opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) + + #opal_os_path_SOURCES = opal_os_path.c + #opal_os_path_LDADD = \ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch new file mode 100644 index 00000000000..dc9b0671658 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch @@ -0,0 +1,25 @@ +On JUWELS, building OpenMPI 5.0.5 with NVHPC 24.9 fails with errors +related to `__ATOMIC_HLE_ACQUIRE` and `__ATOMIC_HLE_RELEASE` not being +defined. Add an additional macro check to let the build succeed. + +--- a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-07-23 01:23:20.567556032 +0200 ++++ a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-10-02 12:19:53.130698758 +0200 +@@ -187,7 +187,7 @@ + * + *********************************************************************/ + +-#if defined(__HLE__) ++#if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) + + # include + +@@ -225,7 +225,7 @@ + __ATOMIC_RELEASE | __ATOMIC_HLE_RELEASE); + } + +-#else /* #if defined(__HLE__) */ ++#else /* #if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) */ + + #include "opal/sys/atomic_impl_spinlock.h" + + From 8cdff853d8e2ea30250c7246d15dc88d2aac2884 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 12:10:10 +0000 Subject: [PATCH 508/524] adding easyconfigs: GLPK-5.0-GCCcore-13.3.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e0bd3088bc8 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [ + ('binutils', '2.41'), +] +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--with-gmp' + + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.a', 'lib/libglpk.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["glpsol --help"] + +moduleclass = 'tools' From a5fd66dbe0034c642e7f27886a85c661a85f13c8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 12:18:23 +0000 Subject: [PATCH 509/524] binutils version --- easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb index e0bd3088bc8..ad96183a02b 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] builddependencies = [ - ('binutils', '2.41'), + ('binutils', '2.42'), ] dependencies = [ ('GMP', '6.3.0'), From cd1f1b9ed7bddd7b0b372265437199a8b7bc8a43 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 16:00:11 +0000 Subject: [PATCH 510/524] adding easyconfigs: Xvfb-21.1.14-GCCcore-13.3.0.eb --- .../x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb | 126 ++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d90dad9791b --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.14' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('libxslt', '1.1.42'), + ('gettext', '0.22.5'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libdrm', '2.4.122'), + ('Mesa', '24.1.3'), + ('nettle', '3.10'), + ('libunwind', '1.8.1'), + ('XZ', '5.4.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.3', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['3a026b468874eb672a1d0a57dbd3ddeda4f0df09886caf97d30097b70c2df3f8'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.1', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['f029ae80cdd75d89bee7f7af61c21e07982adfb9f72344a158b99f91f77ef5ed'], + }), + ('font-misc-misc', '1.1.3', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['00cecc490fcbe2f789cf13c408c459673c2c33ab758d802677321cffcda35373'], + }), + ('xkeyboard-config', '2.43', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['c810f362c82a834ee89da81e34cd1452c99789339f46f6037f4b9e227dd06c01'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.3', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['88c288e0a30bf071631118644f5232cae3a79713a7c82dd31a236e8e2c6fca15'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From 5754839274705a354eb9b86466ad770425755008 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 16:01:35 +0000 Subject: [PATCH 511/524] Update Xvfb-21.1.14-GCCcore-13.3.0.eb --- easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb index d90dad9791b..1ee18273171 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb @@ -99,7 +99,7 @@ components = [ 'sources': ['xorg-server-%(version)s.tar.gz'], 'patches': [('xvfb-run', '.')], 'checksums': [ - 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.9.tar.gz + 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.14.tar.gz 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run ], 'start_dir': 'xorg-server-%(version)s', From 3075e96a66253cbe5f229c0656562b3e55237cfc Mon Sep 17 00:00:00 2001 From: satishskamath <41335185+satishskamath@users.noreply.github.com> Date: Tue, 26 Nov 2024 12:19:24 +0100 Subject: [PATCH 512/524] Update easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb index e92b712357a..72f3e310448 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb @@ -6,7 +6,7 @@ description = """A very powerful performance visualization and analysis tool bas traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] sources = ['wxparaver-%(version)s-src.tar.bz2'] From 2eceb4ba8e53f567f7816194296244d10b112fd2 Mon Sep 17 00:00:00 2001 From: satishskamath <41335185+satishskamath@users.noreply.github.com> Date: Tue, 26 Nov 2024 12:23:54 +0100 Subject: [PATCH 513/524] Rename Paraver-4.11.4-foss-2023a.eb to Paraver-4.11.4-GCC-12.3.0.eb --- ...{Paraver-4.11.4-foss-2023a.eb => Paraver-4.11.4-GCC-12.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/Paraver/{Paraver-4.11.4-foss-2023a.eb => Paraver-4.11.4-GCC-12.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb similarity index 100% rename from easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb rename to easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb From a8a3df3eab0afa38457d05ac7c538dbb83bba17e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Nov 2024 14:13:28 +0100 Subject: [PATCH 514/524] adding easyconfigs: HeFFTe-2.4.1-foss-2023b.eb --- .../h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb new file mode 100644 index 00000000000..7d38225fc55 --- /dev/null +++ b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'HeFFTe' +version = '2.4.1' + +homepage = 'https://icl.utk.edu/fft' +description = "Highly Efficient FFT for Exascale (HeFFTe) library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/icl-utk-edu/heffte/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de2cf26df5d61baac7841525db3f393cb007f79612ac7534fd4757f154ba3e6c'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +build_shared_libs = True + +configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_CUDA=OFF -DHeffte_ENABLE_MKL=OFF" + +# allow oversubscription of MPI ranks to cores, tests are hardcoded to use up to 12 MPI ranks +pretestopts = "export OMPI_MCA_rmaps_base_oversubscribe=true && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libheffte.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/cmake/Heffte', 'share/heffte/examples'], +} + +moduleclass = 'lib' From 39af9ad5bac3bca314750d67b3f1cec6d423dc71 Mon Sep 17 00:00:00 2001 From: PhoenixEmik Date: Tue, 26 Nov 2024 23:24:44 +0800 Subject: [PATCH 515/524] adding easyconfigs: picard-3.3.0-Java-17.eb --- .../p/picard/picard-3.3.0-Java-17.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb new file mode 100644 index 00000000000..8aafd645195 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +# 3.0.0 +# Graham Derryberry (UTK) +# 3.3.0 +# Emik Lin (HKUMed CPOS) +## + +easyblock = 'JAR' + +name = 'picard' +version = '3.3.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '17')] + +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' From 3b51546d614312b70971cc35f8f4bf6d7a498b83 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 27 Nov 2024 16:41:07 +0100 Subject: [PATCH 516/524] adding easyconfigs: MATES-0.1.5-20241121-foss-2023b.eb, anndata-0.11.1-foss-2023b.eb, pybedtools-0.10.0-foss-2023b.eb, BEDTools-2.31.1-GCC-13.2.0.eb --- .../a/anndata/anndata-0.11.1-foss-2023b.eb | 40 ++++++++++++++ .../b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb | 46 ++++++++++++++++ .../MATES/MATES-0.1.5-20241121-foss-2023b.eb | 52 +++++++++++++++++++ .../pybedtools-0.10.0-foss-2023b.eb | 27 ++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb new file mode 100644 index 00000000000..4cfabbf080c --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.11.1' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('array_api_compat', '1.9.1', { + 'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'], + }), +] + +sanity_check_commands = ["natsort --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..ee6ee7885ea --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb @@ -0,0 +1,46 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.1' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e'] + +builddependencies = [ + ('Python', '3.11.5'), +] +dependencies = [ + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb new file mode 100644 index 00000000000..24837326ae2 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.5-20241121' +local_commit = '3846ad5' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('matplotlib', '3.8.2'), + ('anndata', '0.11.1'), + ('pybedtools', '0.10.0'), + ('PyTorch', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """, + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb new file mode 100644 index 00000000000..986d15e5465 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'pybedtools' +version = '0.10.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('BEDTools', '2.31.1'), + ('Pysam', '0.22.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161'], + }), +] + +moduleclass = 'bio' From c99da1e9e026ee4528a51855ad599eb71473ae99 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 27 Nov 2024 16:46:47 +0100 Subject: [PATCH 517/524] update easyblock of pybedtools --- .../p/pybedtools/pybedtools-0.10.0-foss-2023b.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb index 986d15e5465..2f643966cdb 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'pybedtools' version = '0.10.0' @@ -8,6 +8,9 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'foss', 'version': '2023b'} +sources = [SOURCE_TAR_GZ] +checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161'] + dependencies = [ ('Python', '3.11.5'), ('SciPy-bundle', '2023.11'), @@ -16,12 +19,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True -exts_list = [ - (name, version, { - 'checksums': ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161'], - }), -] - moduleclass = 'bio' From e9d7220858e7b3a78ec013f107719832a48f340f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 28 Nov 2024 14:47:02 +0100 Subject: [PATCH 518/524] Update anndata-0.11.1-foss-2023b.eb - add sanity_check_paths --- easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb index 4cfabbf080c..cb2317d16cc 100644 --- a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb +++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb @@ -35,6 +35,11 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = ["natsort --help"] moduleclass = 'bio' From 77487c1abc3806eabcafbad8be280da64b1d12da Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 28 Nov 2024 14:50:29 +0100 Subject: [PATCH 519/524] Update MATES-0.1.5-20241121-foss-2023b.eb - add samtools dep --- easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb index 24837326ae2..b3ea589bf3a 100644 --- a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb @@ -19,6 +19,7 @@ dependencies = [ ('PyTorch', '2.1.2'), ('Pysam', '0.22.0'), ('tqdm', '4.66.2'), + ('SAMtools, '1.19.2), ] use_pip = True From 7345fe3020eab0cb292185ecad611e897d6e3d3c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 28 Nov 2024 14:57:55 +0100 Subject: [PATCH 520/524] Update MATES-0.1.5-20241121-foss-2023b.eb - typo --- .../easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb index b3ea589bf3a..2c87d3d09bf 100644 --- a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb @@ -19,7 +19,7 @@ dependencies = [ ('PyTorch', '2.1.2'), ('Pysam', '0.22.0'), ('tqdm', '4.66.2'), - ('SAMtools, '1.19.2), + ('SAMtools', '1.19.2'), ] use_pip = True From 3ac794d3d2a6e2bebc498976b98e2c61cefaf735 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 28 Nov 2024 16:27:23 +0100 Subject: [PATCH 521/524] adding easyconfigs: OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb --- ...-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..29ca6680eea --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1cf84ac5419456202757a757c5f9a4f5c6ecd05c65783c7976421cfd6020b3b3'] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('NCCL', '2.20.5', versionsuffix), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('UCC-CUDA', '1.2.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 33294cdbf645930f543ee4136435eb7976497b44 Mon Sep 17 00:00:00 2001 From: PhoenixEmik Date: Fri, 29 Nov 2024 10:34:28 +0800 Subject: [PATCH 522/524] adding easyconfigs: CellRanger-9.0.0.eb --- .../c/CellRanger/CellRanger-9.0.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb new file mode 100644 index 00000000000..b25f6cc0d72 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb @@ -0,0 +1,31 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '9.0.0' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +download_instructions = """ +Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +""" +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d57e574630bc0871299ba0e3e3b9a770b572cd35a819c52bfd58403ccd72035d'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger'], + 'dirs': ['bin/rna', 'bin/tenkit'], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' From de79ec74eb076e1aceda5e21235a73c05ed6764c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 29 Nov 2024 09:31:50 +0100 Subject: [PATCH 523/524] nccl was renamed to xccl --- .../OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb index 29ca6680eea..52593680dff 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb @@ -26,7 +26,7 @@ configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-ncc local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] + [ - 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] + 'libexec/osu-micro-benchmarks/xccl/%s' % x for x in ['collective', 'pt2pt'] ] modextrapaths = {'PATH': local_benchmark_dirs} From ff6f2914606b6e60dc5844bf9853925299998488 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 29 Nov 2024 09:55:09 +0100 Subject: [PATCH 524/524] add line about CUDA support to description --- .../u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb index ae39e3c18e8..f8bba051951 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -8,6 +8,8 @@ homepage = 'https://www.openucx.org/' description = """UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}