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..cb2317d16cc --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb @@ -0,0 +1,45 @@ +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_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +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/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' 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/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' 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..2c87d3d09bf --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb @@ -0,0 +1,53 @@ +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'), + ('SAMtools', '1.19.2'), +] + +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/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/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb new file mode 100644 index 00000000000..09dce5c1aab --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -0,0 +1,52 @@ +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, +}] +patches = ['NECI-20230620_segfault.patch'] +checksums = [ + None, + 'f0b5f62e115a1e07d6b90bc66ee9957a5f5d686bef65beba9c2be4bd8f29f0e4', +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +dependencies = [ + ('HDF5', '1.14.0'), +] + +# 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/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 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/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..52593680dff --- /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/xccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' 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..d2efdfa6e27 --- /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', '0.3.1'), # 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/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/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..2f643966cdb --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('BEDTools', '2.31.1'), + ('Pysam', '0.22.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' 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/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' 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..77e022aa0cf --- /dev/null +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -0,0 +1,25 @@ +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'} + +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' 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..f8bba051951 --- /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. + +This module adds the UCC CUDA support. +""" + +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'} + +moduleclass = 'lib' 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'