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

…asyconfigs into 20241128165907_new_pr_imagecodecs202461

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

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTLR'
+version = '2.7.7'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.antlr2.org/'
+description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
+ is a language tool that provides a framework for constructing recognizers,
+ compilers, and translators from grammatical descriptions containing
+ Java, C#, C++, or Python actions."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.antlr2.org/download/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_includes.patch']
+checksums = [
+    '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9',  # antlr-2.7.7.tar.gz
+    'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66',  # ANTLR-2.7.7_includes.patch
+]
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('Java', '21.0.2', '', SYSTEM)]
+
+configopts = '--disable-examples --disable-csharp --disable-python'
+
+sanity_check_paths = {
+    'files': ['bin/antlr', 'bin/antlr-config'],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["antlr --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb

@@ -0,0 +1,31 @@
+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': '13.2.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('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/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb

@@ -0,0 +1,31 @@
+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': '13.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('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/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/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/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-DB-HTS'
+version = '3.01'
+
+homepage = 'https://metacpan.org/release/Bio-DB-HTS'
+description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files"
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/']
+sources = ['Bio-DB-HTS-%(version)s.tar.gz']
+checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42']
+
+builddependencies = [('pkgconf', '2.2.0')]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('BioPerl', '1.7.8'),
+    ('HTSlib', '1.21'),
+]
+
+preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
+
+options = {'modulename': 'Bio::DB::HTS'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb

@@ -0,0 +1,69 @@
+easyblock = 'PythonBundle'
+
+name = 'bakta'
+version = '1.10.1'
+
+homepage = "https://github.com/oschwengers/bakta"
+description = """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids
+ from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations
+ in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('scikit-build-core', '0.9.3'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Biopython', '1.84'),
+    ('PyYAML', '6.0.1'),
+    ('PyHMMER', '0.10.15'),
+    ('matplotlib', '3.8.2'),
+    ('python-isal', '1.6.1'),
+    ('zlib-ng', '2.2.2'),
+    ('archspec', '0.2.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('about_time', '4.2.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['8bbf4c75fe13cbd3d72f49a03b02c5c7dca32169b6d49117c257e7eb3eaee341'],
+    }),
+    ('grapheme', '0.6.0', {
+        'checksums': ['44c2b9f21bbe77cfb05835fec230bd435954275267fea1858013b102f8603cca'],
+    }),
+    ('alive_progress', '3.2.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0677929f8d3202572e9d142f08170b34dbbe256cc6d2afbf75ef187c7da964a8'],
+    }),
+    ('pyCirclize', '1.7.1', {
+        'source_tmpl': SOURCELOWER_PY3_WHL,
+        'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'],
+    }),
+    ('pyrodigal', '3.6.3', {
+        'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'],
+    }),
+    ('xopen', '2.0.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
+    }),
+    (name, version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['82967b4eefd2a1084743211fe955fa394972c2d2c878c6682e00b13dabc5a445'],
+    }),
+]
+
+local_bins = ['bakta', 'bakta_db', 'bakta_io', 'bakta_plot', 'bakta_proteins']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % bin for bin in local_bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['%s --help' % bin for bin in local_bins]
+
+moduleclass = 'tools'

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'

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'

easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'PerlModule'
+
+name = 'Compress-Raw-Zlib'
+version = '2.213'
+
+homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib'
+description = "Low-Level Interface to zlib or zlib-ng compression library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('zlib', '1.3.1'),
+]
+
+options = {'modulename': 'Compress::Raw::Zlib'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'