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

…asyconfigs into 20240122121733_new_pr_ESM-2200

easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '2.3.7'
+
+homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss'
+description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'cstd': 'c++17'}
+
+source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f']
+
+dependencies = [
+    ('Autoconf', '2.71'),
+    ('Automake', '1.16.5'),
+    ('Boost', '1.82.0'),
+    ('sparsehash', '2.0.4'),
+    ('btllib', '1.7.0'),
+]
+
+preconfigopts = "./autogen.sh && "
+configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"'
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+sanity_check_commands = ['ABYSS --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.3'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True, 'openmp': False}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb

@@ -0,0 +1,42 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.3'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {
+    'pic': True,
+    'usempi': True,
+    'openmp': False,
+    'extra_cflags': '-fp-speculation=fast -fp-model fast'
+}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+installopts = '--verbose'
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.22.1'
+
+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': 'iimkl', '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', '3.11.1', {
+        'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'],
+    }),
+    ('ase', version, {
+        'patches': [
+            'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch',
+            'ASE-3.22.1-Compatibility-with-pytest-part-2.patch',
+            'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch',
+            'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch',
+        ],
+        'checksums': [
+            {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'},
+            {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch':
+             '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'},
+            {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch':
+             '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'},
+            {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch':
+             'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'},
+            {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch':
+             '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'},
+        ],
+    }),
+    ('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/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb

@@ -0,0 +1,32 @@
+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': '12.2.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('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'

easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb

@@ -44,18 +44,30 @@ configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
 configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
 configopts += "-DZSTD_ROOT=$EBROOTZSTD "
 
-# also install Python bindings
-local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
-local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
-local_install_pyarrow_cmds += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && "
-local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
-local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && "
-local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
-local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON "
-local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
-local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
-local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ."
-postinstallcmds = [local_install_pyarrow_cmds]
+# install Python bindings
+_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
+_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && "
+_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
+_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON "
+_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
+_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+exts_list = [
+    ('pyarrow', version, {
+        'sources': ['apache-arrow-%(version)s.tar.gz'],
+        'checksums': ['5c70eafb1011f9d124bafb328afe54f62cc5b9280b7080e1e3d668f78c0e407e'],
+        'start_dir': '%(builddir)s/apache-arrow-%(version)s/python',
+        'preinstallopts': _pyarrow_preinstall_opts,
+    }),
+]
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 

easybuild/easyconfigs/a/anvio/anvio-8-foss-2022b.eb

@@ -0,0 +1,111 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'anvio'
+version = '8'
+
+homepage = 'https://merenlab.org/software/anvio/'
+description = """An analysis and visualization platform for 'omics data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+github_account = 'merenlab'
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Pysam', '0.21.0'),
+    ('matplotlib', '3.7.0'),
+    ('scikit-learn', '1.2.1'),
+    ('prodigal', '2.6.3'),
+    ('Biopython', '1.81'),
+    ('h5py', '3.8.0'),
+    ('HMMER', '3.3.2'),
+    ('networkx', '3.0'),
+    ('numba', '0.58.1'),
+    ('statsmodels', '0.14.0'),
+    ('snakemake', '7.32.3'),
+    ('ETE', '3.1.3'),
+    ('dill', '0.3.7'),
+    ('Seaborn', '0.12.2'),
+    ('Levenshtein', '0.24.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('bottle', '0.12.25', {
+        'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'],
+    }),
+    ('colored', '2.2.4', {
+        'checksums': ['595e1dd7f3b472ea5f12af21d2fec8a2ea2cf8f9d93e67180197330b26df9b61'],
+    }),
+    ('asgiref', '3.7.2', {
+        'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'],
+    }),
+    ('sqlparse', '0.4.4', {
+        'checksums': ['d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c'],
+    }),
+    ('Django', '5.0.1', {
+        'checksums': ['8c8659665bc6e3a44fefe1ab0a291e5a3fb3979f9a8230be29de975e57e8f854'],
+    }),
+    ('illumina-utils', '2.13', {
+        'checksums': ['e688ca221ea6178614073b72205fce7b4a54695237c7aa96713492ecd99bd56e'],
+        # python-Levenshtein was renamed to Levenshtein
+        'preinstallopts': "sed -i 's/python-Levenshtein/Levenshtein/g' requirements.txt && ",
+        'modulename': 'IlluminaUtils',
+    }),
+    ('mistune', '3.0.2', {
+        'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'],
+    }),
+    ('multiprocess', '0.70.15', {
+        'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'],
+    }),
+    ('Paste', '3.7.1', {
+        'checksums': ['6d07a8e1c7fa72b8cf403762a002f80d12c0384056956dd0a87cb9a3be64749a'],
+    }),
+    ('plotext', '5.2.8', {
+        'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'],
+    }),
+    ('pyani', '0.2.12', {
+        'checksums': ['4f56b217656f53416b333b69495a4ba8cde782e64e475e1481cb2213ce6b9388'],
+    }),
+    ('rich_argparse', '1.4.0', {
+        'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/merenlab/anvio/releases/download/v%(version)s/'],
+        'patches': ['anvio-8_fix-rU.patch'],
+        'checksums': [
+            {'anvio-8.tar.gz': '13da84d48d7266a8986815efb024772fa26ad1c8a951d42897c3a51e3d924feb'},
+            {'anvio-8_fix-rU.patch': '5eafa5962f59b563cfc3913fb688963b5fe052714c7d7c66b013af065e7a2fea'},
+        ],
+        # remove too strict requirements for Python packages anvio depends on
+        'preinstallopts': "sed -i -e 's/==.*//g' -e 's/<=.*//g' requirements.txt && ",
+    }),
+]
+
+local_binaries_list = [
+    'anvi-pan-genome',
+    'anvi-script-reformat-fasta',
+    'anvi-profile',
+    'anvi-help',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries_list],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "anvi-self-test --suite mini --no-interactive",
+    "anvi-pan-genome --help",
+    "anvi-script-reformat-fasta --help",
+    "anvi-profile --version",
+    "anvi-help --help",
+]
+
+moduleclass = 'bio'