diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb new file mode 100644 index 00000000000..333a0374279 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Java', '21.0.2', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..389e96b3d06 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = [SOURCE_TAR_GZ] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Perl', '5.38.0'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9656cf84761 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = [SOURCE_TAR_GZ] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Perl', '5.38.2'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb new file mode 100644 index 00000000000..490e86bfb7a --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '2.2.0')] + +dependencies = [ + ('Perl', '5.38.2'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.21'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb b/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb new file mode 100644 index 00000000000..89703e6caf7 --- /dev/null +++ b/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'bakta' +version = '1.10.1' + +homepage = "https://github.com/oschwengers/bakta" +description = """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids + from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations + in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), + ('PyYAML', '6.0.1'), + ('PyHMMER', '0.10.15'), + ('matplotlib', '3.8.2'), + ('python-isal', '1.6.1'), + ('zlib-ng', '2.2.2'), + ('archspec', '0.2.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('about_time', '4.2.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8bbf4c75fe13cbd3d72f49a03b02c5c7dca32169b6d49117c257e7eb3eaee341'], + }), + ('grapheme', '0.6.0', { + 'checksums': ['44c2b9f21bbe77cfb05835fec230bd435954275267fea1858013b102f8603cca'], + }), + ('alive_progress', '3.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0677929f8d3202572e9d142f08170b34dbbe256cc6d2afbf75ef187c7da964a8'], + }), + ('pyCirclize', '1.7.1', { + 'source_tmpl': SOURCELOWER_PY3_WHL, + 'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'], + }), + ('pyrodigal', '3.6.3', { + 'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'], + }), + ('xopen', '2.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['82967b4eefd2a1084743211fe955fa394972c2d2c878c6682e00b13dabc5a445'], + }), +] + +local_bins = ['bakta', 'bakta_db', 'bakta_io', 'bakta_plot', 'bakta_proteins'] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%s --help' % bin for bin in local_bins] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb new file mode 100644 index 00000000000..752cc55bb94 --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Cluster-Buster' +version = '20240927' +local_commit = '06fee8b' + +homepage = 'https://github.com/weng-lab/cluster-buster' +description = """Cluster-Buster is a program for finding interesting functional regions, + such as transcriptional enhancers, in DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/weng-lab/cluster-buster/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['a77583ae1f38cc08af551932e5f6b35185fde78db330270bb2eb32ecb4d926cc'] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + 'dirs': [], +} + +sanity_check_commands = ['cbust -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..13ea1eaab8d --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.213' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('zlib', '1.3.1'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb new file mode 100644 index 00000000000..a659656f754 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.7.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + {'v8.7.0.tar.gz': 'd7ab266e2af8c8b230721d4df59e61aa03c612a95cc39c07a2d5695746f21f56'}, + {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'}, +] + +builddependencies = [('CMake', '3.29.3')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.7.4'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb index af01c621328..9f66e2f8724 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'enchant-2' version = '2.6.5' -homepage = 'https://github.com/AbiWord/enchant' +homepage = 'http://rrthomas.github.io/enchant/' description = """Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific @@ -15,7 +15,7 @@ be added without needing any change to the program using Enchant.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +source_urls = ['https://github.com/rrthomas/enchant/releases/download/v%(version)s'] sources = ['enchant-%(version)s.tar.gz'] checksums = ['9e8fd28cb65a7b6da3545878a5c2f52a15f03c04933a5ff48db89fe86845728e'] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb new file mode 100644 index 00000000000..7f78472bcea --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb @@ -0,0 +1,56 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University +# Update: Petr Král (INUITS) + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.3.6' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.3.5_use_EB_LSD2.patch', +] +checksums = [ + {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'}, + {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef7029f258f --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.21.0-131' + +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://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c06b30e108608bc40dcb15df57302af4511023801dca004edb3f2df2cc0a72cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('libxml2', '2.12.7'), + ('libtirpc', '1.3.5'), + ('PCRE', '8.45'), + ('util-linux', '2.40'), +] + +preconfigopts = "autoreconf -fi && " +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/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..20f151d30e1 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.9' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884'] + +builddependencies = [ + ('binutils', '2.42'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb new file mode 100644 index 00000000000..cf83d365785 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.2.9' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6245886e2a18a4821b0fb768cf9906de09aeb47c303462c8e85f0d1a4f34956d'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.6.2'), + ('ANTLR', '2.7.7', '-Java-21.0.2'), + ('libdap', '3.21.0-131'), + ('GSL', '2.8'), + ('netCDF', '4.9.2'), + ('ESMF', '8.7.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb new file mode 100644 index 00000000000..75b0cb4a2d6 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '24.10.2' + +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-dist'] +checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475'] + +dependencies = [('Java', '21')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", + "nextflow info", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb new file mode 100644 index 00000000000..2d6165976d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb @@ -0,0 +1,47 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyHMMER' +version = '0.10.15' + +homepage = 'https://github.com/althonos/pyhmmer' +description = """ +HMMER is a biological sequence analysis tool that uses profile hidden Markov +models to search for sequence homologs. HMMER3 is developed and maintained by +the Eddy/Rivas Laboratory at Harvard University. + +pyhmmer is a Python package, implemented using the Cython language, that +provides bindings to HMMER3. It directly interacts with the HMMER internals, +which has the following advantages over CLI wrappers (like hmmer-py)""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('HMMER', '3.4'), + ('psutil', '6.1.0') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('%(namelower)s', version, { + # Requirement for `psutil` is too strict. + 'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ", + 'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5ba7c5d9380 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '6.1.0' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': ['release-%(version)s.tar.gz'], + 'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb new file mode 100644 index 00000000000..89191292693 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = 'c3f65d7' +version = '2024-01-28' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'foss', 'version': '2023a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2024-01-28.tar.gz': '9828dcdde92b9627cfe888b5be530040c1c51c97f5a3c930d82ef24d862610e3'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PySCF', '2.7.0'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "sed -i 's/ -undefined dynamic_lookup//g' src/Makefile && " +prebuildopts += "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c76c4f5371b --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.7.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bf658f4aaf815d9d03c8121650b6f0b8067265c36e31bc6660b98ef144d81813'] + +builddependencies = [ + ('binutils', '2.42'), + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('PROJ', '9.4.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..254e2c6a8b9 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '3.6.1' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pytest', '8.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '3.0.2', { + 'checksums': ['c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d'], + }), + ('execnet', '2.1.1', { + 'checksums': ['5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3'], + }), + (name, version, { + 'modulename': 'xdist', + 'source_tmpl': 'pytest_xdist-%(version)s.tar.gz', + 'checksums': ['ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0701b7af348 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '8.3.3' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +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'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '8.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('flit-core', '3.10.1', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['66e5b87874a0d6e39691f0e22f09306736b633548670ad3c09ec9db03c5662f7'], + }), + ('hypothesis', '6.119.0', { + 'checksums': ['ca441c6ef55d17f27f642fa08657e80f9c13d9da7ae191c8ad58fbc2f16acd1b'], + }), + ('elementpath', '4.6.0', { + 'checksums': ['ba46bf07f66774927727ade55022b6c435fac06b2523cb3cd7689a1884d33468'], + }), + ('xmlschema', '3.4.3', { + 'checksums': ['0c638dac81c7d6c9da9a8d7544402c48cffe7ee0e13cc47fc0c18794d1395dfb'], + }), + (name, version, { + 'checksums': ['70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch new file mode 100644 index 00000000000..d2a91a510b6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch @@ -0,0 +1,30 @@ +Fix line length greather than 132 characters. +Also fix the use of ZGEMM3M, which is not available in the FlexiBLAS library. +See https://github.com/anharmonic/d3q/issues/22 +--- a/d3q/thermal2/PROGRAM_r2q.f90 ++++ b/d3q/thermal2/PROGRAM_r2q.f90 +@@ -744,7 +744,8 @@ PROGRAM r2q + + + WRITE(*,'(2x,a,f12.8)') "Note: q-point and path length in units of 2pi/alat, conversion to bohr^-1: ", S%tpiba +- WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 ++ WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", & ++ 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 + + IF( input%calculation=="dos") THEN + CALL PH_DOS(input,S,fc2) +diff --git a/thermal2/functions.f90 b/thermal2/functions.f90 +index 90d8a90..9e9adb2 100644 +--- a/d3q/thermal2/functions.f90 ++++ b/d3q/thermal2/functions.f90 +@@ -465,8 +465,8 @@ end subroutine quicksort_idx + ! + !rotate_d2 = MATMUL(TRANSPOSE(CONJG(U)), MATMUL(D,U)) + ! +- CALL ZGEMM3M('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) +- CALL ZGEMM3M('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) ++ CALL ZGEMM('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) ++ CALL ZGEMM('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) + ! + END FUNCTION + ! diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb new file mode 100644 index 00000000000..f017367700b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb @@ -0,0 +1,147 @@ +name = 'QuantumESPRESSO' +version = '7.4' + +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 = "89a3cc199c0a200c9f0f688c3229ef6b9a8d63bd" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.4, see https://github.com/anharmonic/d3q/issues/22 +local_d3q_hash = "808acbaf012468f42147d8d6af452ec64b9e5ab0" +# Different from the one at tag qe-7.4 +local_qe_gipaw_hash = "9b2ae1a46cae045cc04ef02c1072f2e1e74873b2" +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, + }, + }, +] +patches = [ + { + 'name': 'QuantumESPRESSO-7.4-d3q.patch', + 'sourcepath': '../' # Needed as patches are normally applied to the first `finalpath` directory + }, +] +# Holding off git clone checksum checks untill 5.0.x +# See https://github.com/easybuilders/easybuild-framework/pull/4248 +checksums = [ + 'b15dcfe25f4fbf15ccd34c1194021e90996393478226e601d876f7dea481d104', + None, None, None, None, None, None, None, None, + '1f1686365fbf0cc56f634e072a92b3d336fe454348e514d0b4136d447f0d4923' +] + +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 = ( + 0.98 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [] diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..acc1705405e --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb new file mode 100644 index 00000000000..1996303d91d --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb @@ -0,0 +1,44 @@ +name = 'VEP' +version = '113.3' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ee68013eb035e17129e8f69977f525ebdd8321e73b3164a7bda6e103e2d10beb'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.051'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.213'), +] + +# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed +# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) +species = 'cyprinus_carpio_carpio' + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +sanity_check_commands = ['vep --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3ea3731df79 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] +dependencies = [('Python', '3.11.5')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb b/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb new file mode 100644 index 00000000000..66965fa2a54 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2024.11.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +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, { + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['1ccace44573ddb862e210ad3ec204210654d2c750bec11bbe7d842dfc298591f'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b611b7c7304 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.42'), + ('xorg-macros', '1.20.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8e1cf20a94d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.2' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.1', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools'