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

…asyconfigs into wrf-4.6.1

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/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/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'

easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb

@@ -0,0 +1,37 @@
+name = 'ESMF'
+version = '8.7.0'
+
+homepage = 'https://www.earthsystemcog.org/projects/esmf/'
+description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing
+ high-performance, multi-component Earth science modeling applications."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True}
+
+source_urls = ['https://github.com/esmf-org/esmf/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['ESMF-6.1.1_libopts.patch']
+checksums = [
+    {'v8.7.0.tar.gz': 'd7ab266e2af8c8b230721d4df59e61aa03c612a95cc39c07a2d5695746f21f56'},
+    {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'},
+]
+
+builddependencies = [('CMake', '3.29.3')]
+
+dependencies = [
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('netCDF-C++4', '4.3.1'),
+    ('libarchive', '3.7.4'),
+]
+
+# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour)
+prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"'
+
+buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
+buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"'
+
+# too parallel causes the build to become really slow
+maxparallel = 8
+
+moduleclass = 'geo'

easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb

@@ -6,7 +6,7 @@ easyblock = 'ConfigureMake'
 name = 'enchant-2'
 version = '2.6.5'
 
-homepage = 'https://github.com/AbiWord/enchant'
+homepage = 'http://rrthomas.github.io/enchant/'
 description = """Enchant aims to provide a simple but comprehensive abstraction for dealing
 with different spell checking libraries in a consistent way. A client, such
 as a text editor or word processor, need not know anything about a specific
@@ -15,7 +15,7 @@ be added without needing any change to the program using Enchant."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s']
+source_urls = ['https://github.com/rrthomas/enchant/releases/download/v%(version)s']
 sources = ['enchant-%(version)s.tar.gz']
 checksums = ['9e8fd28cb65a7b6da3545878a5c2f52a15f03c04933a5ff48db89fe86845728e']
 

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb

@@ -0,0 +1,56 @@
+# Updated to v2.1.3 by
+# R.QIAO <[email protected]>
+# DeepThought, Flinders University
+# Update: Petr Král (INUITS)
+
+easyblock = 'CMakeMake'
+
+name = 'IQ-TREE'
+version = '2.3.6'
+
+# HTTPS is not working
+homepage = 'http://www.iqtree.org/'
+description = """Efficient phylogenomic software by maximum likelihood"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
+
+source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'IQ-TREE-2.3.5_use_EB_LSD2.patch',
+]
+checksums = [
+    {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'},
+    {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Eigen', '3.4.0'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
+    ('LSD2', '2.4.1'),
+]
+
+local_conf_opts = ' -DUSE_LSD2=ON '
+configopts = [
+    '-DIQTREE_FLAGS=omp' + local_conf_opts,
+    '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts,
+]
+
+sanity_check_paths = {
+    'files': ['bin/iqtree2', 'bin/iqtree2-mpi'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "iqtree2 --help",
+    "mkdir -p $TMPDIR/{test-omp,test-mpi}",
+    "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo",
+    "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo",
+]
+
+moduleclass = 'bio'