Merge branch 'easybuilders:develop' into Bio-SearchIO-hmmer

easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb

@@ -0,0 +1,27 @@
+name = 'Advisor'
+version = '2025.0.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/advisor.html'
+description = """Vectorization Optimization and Thread Prototyping
+ - Vectorize & thread code or performance “dies”
+ - Easy workflow + data + tips = faster code faster
+ - Prioritize, Prototype & Predict performance gain
+ """
+
+toolchain = SYSTEM
+
+source_urls = [
+    'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/fe95ae4a-3692-4e31-919d-3e7bdf5832f1/']
+sources = ['intel-advisor-%(version)s.798_offline.sh']
+checksums = ['bf85d4b0bd199a2babdff6b4bd3885ce569a3ad0e992b99b2e14dbb30af88cd4']
+
+dontcreateinstalldir = True
+
+sanity_check_paths = {
+    'files': ['%(namelower)s/%(version_major_minor)s/bin64/advisor'],
+    'dirs': ['%(namelower)s/%(version_major_minor)s/bin64',
+             '%(namelower)s/%(version_major_minor)s/lib64',
+             '%(namelower)s/%(version_major_minor)s/include/intel64']
+}
+
+moduleclass = 'perf'

easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'PythonBundle'
+
+name = 'absl-py'
+version = '2.1.0'
+
+homepage = 'https://github.com/abseil/abseil-py'
+description = """absl-py is a collection of Python library code for building Python
+applications. The code is collected from Google's own Python code base, and has
+been extensively tested and used in production."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('Python', '3.12.3')]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', version, {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

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'

easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb

@@ -0,0 +1,36 @@
+# Authors:: Richard Lawrence  <[email protected]> - TAMU HPRC - https://hprc.tamu.edu
+
+easyblock = 'CMakeMake'
+
+name = 'assimp'
+version = '5.4.3'
+
+homepage = 'https://github.com/assimp/assimp'
+description = """
+ Open Asset Import Library (assimp) is a library to import and export various
+ 3d-model-formats including scene-post-processing to generate missing render data.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['66dfbaee288f2bc43172440a55d0235dfc7bf885dda6435c038e8000e79582cb']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('CMake', '3.29.3'),
+    ('zlib', '1.3.1'),
+]
+
+# workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315
+configopts = "-DASSIMP_WARNINGS_AS_ERRORS=OFF "
+
+
+sanity_check_paths = {
+    'files': ['include/%(name)s/types.h', 'lib/libassimp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

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'

easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb

@@ -0,0 +1,73 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+# we recommend to use --download-timeout=1000 when fetching the files
+
+easyblock = 'CmdCp'
+
+name = 'BGEN-enkre'
+version = '1.1.7'
+
+homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk'
+description = """This repository contains a reference implementation 
+of the BGEN format, written in C++. The library can be used as the 
+basis for BGEN support in other software, or as a reference for 
+developers writing their own implementations of the BGEN format.
+Please cite:
+Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", 
+bioArxiv 308296; doi: https://doi.org/10.1101/308296
+"""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/']
+sources = ['v%(version)s.tgz']
+patches = [
+    '3rd-party-removal.patch',
+    'BGEN-enkre_streampos.patch',
+]
+
+checksums = [
+    ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3',  # v1.1.7.tgz
+     'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'),
+    '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767',  # 3rd-party-removal.patch
+    '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869',  # BGEN-enkre_streampos.patch
+]
+
+builddependencies = [
+    ('Python', '3.11.3'),
+]
+
+dependencies = [
+    ('SQLite', '3.42.0'),
+    ('zstd', '1.5.5'),
+    ('Boost', '1.55.0'),
+]
+
+cmds_map = [
+    ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&"
+     " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&"
+     "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] "
+     " >> build/c4che/_cache.py && ./waf"),
+]
+
+files_to_copy = [
+    (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'),
+    (['build/db/libdb.a', 'build/libbgen.a'], 'lib'),
+    (['genfile/include/*', 'db/include/*'], 'include'),
+]
+
+postinstallcmds = ['./build/test/unit/test_bgen']
+
+sanity_check_paths = {
+    'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'],
+    'dirs': ['bin', 'lib', 'include'],
+}
+
+sanity_check_commands = [
+    'bgenix -help',
+    'cat-bgen -help',
+    'edit-bgen -help',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb

@@ -0,0 +1,26 @@
+name = 'Bazel'
+version = '7.4.1'
+
+homepage = 'https://bazel.io/'
+description = """Bazel is a build tool that builds code quickly and reliably.
+It is used to build the majority of Google's software."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s']
+sources = ['%(namelower)s-%(version)s-dist.zip']
+checksums = ['83386618bc489f4da36266ef2620ec64a526c686cf07041332caff7c953afaf5']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+    ('Zip', '3.0'),
+]
+dependencies = [
+    ('Java', '21.0.2', '', SYSTEM),
+]
+
+runtest = True
+testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..."
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb

@@ -0,0 +1,89 @@
+easyblock = 'Tarball'
+
+name = 'BindCraft'
+version = '1.1.0'
+
+homepage = 'https://github.com/martinpacesa/BindCraft'
+description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta.
+ Select your target and let the script do the rest of the work and finish once you have enough designs to order!"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}]
+checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('Seaborn', '0.13.2'),
+    ('tqdm', '4.66.1'),
+    ('OpenMM', '8.0.0'),
+    ('FFmpeg', '6.0'),
+    ('matplotlib', '3.7.2'),
+    ('PyRosetta', '4.release-387'),
+    ('jax', '0.4.25'),
+    ('dm-haiku', '0.0.13'),
+    ('dm-tree', '0.1.8'),
+    ('ml-collections', '0.1.1'),
+    ('Optax', '0.2.2'),
+    ('py3Dmol', '2.1.0'),
+    ('JupyterLab', '4.0.5'),
+    ('hatchling', '1.18.0'),
+    ('Flax', '0.8.4'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+exts_list = [
+    ('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'],
+    }),
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    # older version compatible with `jupyterlab-4.0.5`
+    ('notebook', '7.0.8', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'],
+    }),
+    ('jupyter', '1.1.1', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'],
+    }),
+    ('immutabledict', '4.2.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'],
+    }),
+    ('colabdesign', '1.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'],
+    }),
+]
+
+fix_python_shebang_for = ['bindcraft.py']
+
+postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py']
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_paths = {
+    'files': ['bindcraft.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["bindcraft.py --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb

@@ -0,0 +1,21 @@
+name = 'Boost'
+version = '1.55.0'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.13'),
+]
+
+configopts = '--without-libraries=python'
+
+moduleclass = 'devel'