Merge branch 'easybuilders:develop' into easybuild-easyconfigs-Archiv…

…e-Zip

easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-12.3.0.eb

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+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <[email protected]>, Thekla Loizou <[email protected]>
+# Contributors:: Alex Domingo (Vrije Universiteit Brussel)
+# License::   MIT/GPL
+#
+##
+
+name = 'BLAT'
+version = '3.7'
+
+homepage = 'https://genome.ucsc.edu/goldenPath/help/blatSpec.html'
+description = """BLAT on DNA is designed to quickly find sequences of 95% and
+greater similarity of length 25 bases or more."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://genome-test.gi.ucsc.edu/~kent/src/']
+sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
+patches = ['BLAT-%(version)s_mend-tests.patch']
+checksums = [
+    {'blatSrc37.zip': '88ee2b272d42ab77687c61d200b11f1d58443951069feb7e10226a2509f84cf2'},
+    {'BLAT-3.7_mend-tests.patch': '1f42c7fadf7676a5cc3a2016f70089c3541aa1d53816cf86072682c44cf311a6'},
+]
+
+# BLAT relies on a bundled old version of HTSlib. We use the bundled library
+# because it is statically linked and the newer HTSlib in this toolchain is not
+# API compatible with it.
+dependencies = [
+    ('freetype', '2.13.0'),
+    ('libiconv', '1.17'),
+    ('libpng', '1.6.39'),
+    ('MariaDB', '11.6.0'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('util-linux', '2.39'),
+    ('zlib', '1.2.13'),
+]
+
+pretestopts = 'PATH="%(builddir)s/blatSrc/bin:$PATH"'
+runtest = 'test'
+
+_blat_bins = ["blat", "faToNib", "faToTwoBit", "gfClient", "gfServer", "nibFrag", "pslPretty",
+              "pslReps", "pslSort", "twoBitInfo", "twoBitToFa"]
+
+files_to_copy = [(["bin/%s" % x for x in _blat_bins] + ["webBlat/webBlat"], 'bin')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in _blat_bins + ["webBlat"]],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb

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+# 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': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+# https://github.com/pezmaster31/bamtools
+github_account = 'pezmaster31'
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/COLMAP/COLMAP-3.8-foss-2022b.eb

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+easyblock = 'CMakeNinja'
+
+name = 'COLMAP'
+version = '3.8'
+
+homepage = 'https://colmap.github.io'
+description = """COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline
+with a graphical and command-line interface"""
+
+source_urls = ['https://github.com/colmap/colmap/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['02288f8f61692fe38049d65608ed832b31246e7792692376afb712fa4cef8775']
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Ninja', '1.11.1'),
+    ('Eigen', '3.4.0'),
+    ('googletest', '1.12.1'),
+]
+
+dependencies = [
+    ('Boost', '1.81.0'),
+    ('Qt5', '5.15.7'),
+    ('FLANN', '1.9.2'),
+    ('FreeImage', '3.18.0'),
+    ('METIS', '5.1.0'),
+    ('glog', '0.6.0'),
+    ('SQLite', '3.39.4'),
+    ('glew', '2.2.0', '-egl'),
+    ('CGAL', '5.5.2'),
+    ('Ceres-Solver', '2.2.0'),
+]
+
+configopts = "-DCMAKE_CXX_STANDARD=17"
+
+sanity_check_paths = {
+    'files': ['bin/colmap', 'lib/colmap/libcolmap.a', 'lib/colmap/libpba.a', 'lib/colmap/libvlfeat.a'],
+    'dirs': ['include/colmap'],
+}
+
+sanity_check_commands = ["colmap -h"]
+
+moduleclass = 'vis'

easybuild/easyconfigs/c/CREST/CREST-3.0.2-gfbf-2023b.eb

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+easyblock = 'CMakeMake'
+
+name = 'CREST'
+version = '3.0.2'
+
+homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html'
+description = """CREST is an utility/driver program for the xtb program. Originally it was designed
+ as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool,
+ but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally
+ the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb
+ program) and tool for the creation and analysation of structure ensembles.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchainopts = {'opt': True}
+
+sources = [{
+    'filename': SOURCE_TAR_GZ,
+    'git_config': {
+        'url': 'https://github.com/crest-lab',
+        'repo_name': 'crest',
+        'tag': 'v%s' % version,
+        'recursive': True,
+    },
+}]
+checksums = [None]
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('dftd4', '3.7.0'),
+    ('mctc-lib', '0.3.1'),
+    ('mstore', '0.3.0'),
+    ('multicharge', '0.3.0'),
+    ('xtb', '6.7.1'),
+]
+
+runtest = "test"
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["crest -h", "crest --cite"]
+
+moduleclass = 'chem'

easybuild/easyconfigs/c/Ceres-Solver/Ceres-Solver-2.2.0-foss-2022b.eb

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+easyblock = 'CMakeMake'
+
+name = 'Ceres-Solver'
+version = '2.2.0'
+
+homepage = 'http://ceres-solver.org'
+description = """Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization
+problems"""
+
+source_urls = ['http://ceres-solver.org/']
+sources = ['ceres-solver-%(version)s.tar.gz']
+checksums = ['48b2302a7986ece172898477c3bcd6deb8fb5cf19b3327bc49969aad4cede82d']
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Eigen', '3.4.0'),
+]
+
+dependencies = [
+    ('glog', '0.6.0'),
+    ('gflags', '2.2.2'),
+    ('SuiteSparse', '5.13.0', '-METIS-5.1.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libceres.a'],
+    'dirs': ['include/ceres', 'lib/cmake/Ceres'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-gfbf-2023b.eb

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+# A. Domingo (Vrije Universiteit Brussel)
+# J. Sassmannshausen (Imperial College London/UK)
+# C. Willemyns  (Vrije Universiteit Brussel)
+
+easyblock = 'CMakeNinja'
+
+name = 'dftd4'
+version = '3.7.0'
+
+homepage = 'https://dftd4.readthedocs.io'
+description = """
+The dftd4 project provides an implementation of the generally applicable, charge dependent
+London-dispersion correction, termed DFT-D4.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchainopts = {'openmp': True}
+
+github_account = 'dftd4'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('mctc-lib', '0.3.1'),
+    ('mstore', '0.3.0'),
+    ('multicharge', '0.3.0'),
+]
+
+build_shared_libs = True
+
+configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1'
+
+# run suite of tests with ctest
+test_cmd = 'ctest'
+runtest = ''
+
+sanity_check_paths = {
+    'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'],
+    'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'],
+}
+
+sanity_check_commands = ["dftd4 --help"]
+
+moduleclass = 'chem'

easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2022b.eb

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+# 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': '2022b'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/mariusmuja/flann/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['e26829bb0017f317d9cc45ab83ddcb8b16d75ada1ae07157006c1e7d601c8824']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('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'

easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.2.0.eb

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+easyblock = 'CMakeMake'
+
+name = 'gflags'
+version = '2.2.2'
+
+homepage = 'https://github.com/gflags/gflags'
+description = """
+The gflags package contains a C++ library that implements commandline flags
+processing.  It includes built-in support for standard types such as string
+and the ability to define flags in the source file in which they are used.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/gflags/gflags/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON'
+
+sanity_check_paths = {
+    'files': ['bin/gflags_completions.sh'] +
+             ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT,
+                                     'libgflags.a', 'libgflags_nothreads.a']] +
+             ['include/gflags/gflags_completions.h'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.2.0-egl.eb

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+easyblock = 'ConfigureMake'
+versionsuffix = '-egl'
+# available: -glx, -osmesa, -egl
+# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and   
+# offscreen), and OSMESA (offscreen software only).
+
+name = 'glew'
+version = '2.2.0'
+
+homepage = 'https://github.com/nigels-com/glew'
+description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source
+C/C++ extension loading library. GLEW provides efficient run-time mechanisms
+for determining which OpenGL extensions are supported on the target platform."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/']
+sources = ['%(name)s-%(version)s.tgz']
+checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Mesa', '22.2.4'),
+    ('X11', '20221110'),
+]
+
+local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`'
+buildopts = local_system
+
+skipsteps = ['configure']
+
+preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s '
+install_cmd = 'make install.all ' + local_system
+
+sanity_check_paths = {
+    'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] +
+             ['bin/glewinfo', 'bin/visualinfo'] +
+             ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']],
+    'dirs': []
+}
+
+moduleclass = 'devel'