Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20241203174341_new_pr_Scalasca261

.github/workflows/unit_tests.yml

@@ -28,7 +28,7 @@ jobs:
 
     - name: Cache source files in /tmp/sources
       id: cache-sources
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: /tmp/sources
         key: eb-sourcepath

easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2405.eb

@@ -0,0 +1,33 @@
+name = 'ABAQUS'
+version = '2024'
+local_hotfix = '2405'
+versionsuffix = '-hotfix-%s' % local_hotfix
+
+homepage = 'https://www.simulia.com/products/abaqus_fea.html'
+description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
+ dynamics FEA."""
+
+toolchain = SYSTEM
+
+sources = [
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar',
+    # hotfixes
+    '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix,
+]
+checksums = [
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.1-6.tar': 'a8fcd10541a90177aefe68f0dee2a675a56cb97e1fdf4fb7d864b41d594f8b19'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.2-6.tar': '6caffc60ee34351203ac4205b4fcdc7e9975842e35d3ce689b831f94929ddac4'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.3-6.tar': '3d3bc97c686af0c87c4b6e46ae330983ed515bcc180dd30a834811c458774347'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.4-6.tar': 'c62596bd99125475e97bdeccd71baaf7cb36322e8da4d0dd1e4029bac677be16'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.5-6.tar': 'ee3349b2407b5d8a315108656590f39890d82c47085235b847103e22fba96fea'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.6-6.tar': '482829b1c364966ae01a577233bddf6b377b8e3cd9b7f77dd95830d4636677d7'},
+    {'2024.FP.CFA.2405.Part_SIMULIA_EstPrd.Linux64.tar':
+     '70231acf27506546174b896b6724f27a14673594b791eb62fb4c1e3b24ba1852'},
+]
+
+moduleclass = 'cae'

easybuild/easyconfigs/a/ABINIT/ABINIT-10.2.5-intel-2023a.eb

@@ -0,0 +1,67 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '10.2.5'
+
+homepage = 'https://www.abinit.org/'
+description = """
+ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of
+systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a planewave or wavelet basis.
+"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': True, 'pic': True}
+
+source_urls = ['https://forge.abinit.org/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4f72fa457056617e6ed94db21264507eda66cc50224c7ed96b990d6b82de9ac1']
+
+builddependencies = [
+    ('Python', '3.11.3'),
+]
+dependencies = [
+    ('libxc', '6.2.2'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('HDF5', '1.14.0'),
+    ('Wannier90', '3.1.0'),
+]
+
+# Ensure MPI with intel wrappers.
+configopts = '--with-mpi="yes" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# Enable OpenMP
+configopts += '--enable-openmp="yes" '
+
+# BLAS/Lapack from MKL
+configopts += '--with-linalg-flavor=mkl '
+
+# FFTW from MKL
+configopts += '--with-fft-flavor=dfti '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# Wannier90
+preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && '
+
+# Enable double precision for GW calculations
+configopts += '--enable-gw-dpc '
+
+# 'make check' is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb

@@ -0,0 +1,41 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'Tarball'
+
+name = 'ABRicate'
+version = '1.0.0'
+
+homepage = 'https://github.com/tseemann/abricate'
+description = "Mass screening of contigs for antimicrobial and virulence genes"
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+# https://github.com/tseemann/abricate
+github_account = 'tseemann'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('any2fasta', '0.4.2'),
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.16.0'),
+]
+
+postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']
+
+sanity_check_paths = {
+    'files': ['bin/abricate', 'bin/abricate-get_db'],
+    'dirs': ['db'],
+}
+
+sanity_check_commands = [
+    "abricate --help",
+    "abricate --list",
+]
+
+modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb → easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb

@@ -22,7 +22,7 @@ checksums = [
 
 builddependencies = [('binutils', '2.42')]
 
-dependencies = [('Java', '21.0.2', '', SYSTEM)]
+dependencies = [('Java', '17', '', SYSTEM)]
 
 configopts = '--disable-examples --disable-csharp --disable-python'
 

easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2023a.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.24.0'
+
+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': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Flask', '2.3.3'),
+    ('matplotlib', '3.7.2'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '2.1.0'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.14.0', {
+        'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'],
+    }),
+    ('ase', version, {
+        'checksums': ['9acc93d6daaf48cd27b844c56f8bf49428b9db0542faa3cc30d9d5b8e1842195'],
+    }),
+    ('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'

easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.24.0'
+
+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': ['9acc93d6daaf48cd27b844c56f8bf49428b9db0542faa3cc30d9d5b8e1842195'],
+    }),
+    ('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'

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,121 @@
+# created by Denis Kristak (Inuits)
+# update: Thomas Hoffmann, EMBL
+easyblock = 'PythonBundle'
+
+name = 'AlphaPulldown'
+version = '2.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/KosinskiLab/AlphaPulldown'
+description = """AlphaPulldown is a Python package that streamlines protein-protein
+interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('Kalign', '3.4.0'),
+    ('PyYAML', '6.0'),
+    ('jax', '0.4.25', versionsuffix),  # also provides absl-py
+    ('Biopython', '1.83'),
+    ('h5py', '3.9.0'),
+    ('IPython', '8.14.0'),
+    ('matplotlib', '3.7.2'),
+    # ('TensorFlow', '2.15.1', versionsuffix),
+    ('TensorFlow', '2.13.0'),  # to be consistent with AF2 ?
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('tqdm', '4.66.1'),
+    ('dm-tree', '0.1.8'),
+    ('py3Dmol', '2.1.0'),
+    ('HMMER', '3.4'),
+    ('HH-suite', '3.3.0'),
+    ('dm-haiku', '0.0.12', versionsuffix),
+    ('Uni-Core', '0.0.3', versionsuffix),
+    ('JupyterLab', '4.0.5'),
+]
+local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31'
+use_pip = True
+
+local_tests = [
+    'custom_db',
+    'remove_clashes_low_plddt',
+    'modelcif',
+    'features_with_templates',
+    'post_prediction',
+    # require pyrosetta, analysis aptainer image, and AlphaFold2 data:
+    # 'pdb_analyser',
+    # 'get_good_inter_pae',
+]
+local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """
+exts_list = [
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml-collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'sources': ['ml_collections-%(version)s.tar.gz'],
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+    ('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'],
+    }),
+    ('ihm', '1.3', {
+        'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'],
+    }),
+    ('modelcif', '1.0', {
+        'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'],
+    }),
+    ('looseversion', '1.1.2', {
+        'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('biopandas', '0.5.1.dev0', {
+        'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
+    (name, version, {
+        'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ",
+        'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)),
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/KosinskiLab',
+                'repo_name': 'AlphaPulldown',
+                'tag': version, 'recursive': True
+            }
+        }],
+        'testinstall': True,
+        # This needs to be [None], at least until EB v5 is out
+        # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'],
+        'checksums': [None],
+    }),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py',
+              'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
+}
+
+sanity_check_commands = [
+    "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'",
+    "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'",
+]
+
+moduleclass = 'bio'