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

…asyconfigs into 20241129155549_new_pr_Molden73

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/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'

easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'makedepend'
+version = '1.0.9'
+
+homepage = 'https://linux.die.net/man/1/makedepend'
+description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [XORG_UTIL_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('xproto', '7.0.31'),
+    ('xorg-macros', '1.20.1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/makedepend'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb

@@ -0,0 +1,36 @@
+easyblock = 'Binary'
+
+name = 'Nextflow'
+version = '24.10.2'
+
+homepage = 'https://www.nextflow.io/'
+description = """Nextflow is a reactive workflow framework and a programming DSL
+ that eases writing computational pipelines with complex data"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/']
+sources = ['nextflow-%(version)s-dist']
+checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475']
+
+dependencies = [('Java', '21')]
+
+install_cmds = [
+    "mkdir -p %(installdir)s/bin",
+    "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin",
+    "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow",
+    "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist",
+]
+
+sanity_check_paths = {
+    'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "nextflow -v",
+    "nextflow help",
+    "nextflow info",
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb

@@ -0,0 +1,47 @@
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/02
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'PyHMMER'
+version = '0.10.15'
+
+homepage = 'https://github.com/althonos/pyhmmer'
+description = """
+HMMER is a biological sequence analysis tool that uses profile hidden Markov    
+models to search for sequence homologs. HMMER3 is developed and maintained by   
+the Eddy/Rivas Laboratory at Harvard University.
+
+pyhmmer is a Python package, implemented using the Cython language, that        
+provides bindings to HMMER3. It directly interacts with the HMMER internals,    
+which has the following advantages over CLI wrappers (like hmmer-py)"""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+builddependencies = [
+    ('Cython', '3.0.10'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('HMMER', '3.4'),
+    ('psutil', '6.1.0')
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('%(namelower)s', version, {
+        # Requirement for `psutil` is too strict.
+        'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ",
+        'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'psutil'
+version = '6.1.0'
+
+homepage = 'https://github.com/giampaolo/psutil'
+description = """A cross-platform process and system utilities module for Python"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Python', '3.11.5')]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/giampaolo/psutil/archive'],
+        'sources': ['release-%(version)s.tar.gz'],
+        'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb

@@ -0,0 +1,73 @@
+easyblock = 'MakeCp'
+
+name = 'pyWannier90'
+local_commit = 'c3f65d7'
+version = '2024-01-28'
+
+homepage = 'https://github.com/hungpham2017/pyWannier90'
+description = "A Wannier90 Python interface for VASP and PySCF"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+local_wannier90_version = '3.1.0'
+
+sources = [
+    {
+        'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'],
+        'download_filename': '%s.tar.gz' % local_commit,
+        'filename': SOURCE_TAR_GZ
+    },
+    {
+        'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'],
+        'download_filename': 'v%s.tar.gz' % local_wannier90_version,
+        'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version,
+    },
+]
+checksums = [
+    {'pyWannier90-2024-01-28.tar.gz': '9828dcdde92b9627cfe888b5be530040c1c51c97f5a3c930d82ef24d862610e3'},
+    {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'},
+]
+
+builddependencies = [
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PySCF', '2.7.0'),
+]
+
+local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" '
+local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"'
+
+prebuildopts = "sed -i 's/ -undefined dynamic_lookup//g' src/Makefile && "
+prebuildopts += "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version
+prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && "
+prebuildopts += local_wannier90_make + " && "
+prebuildopts += local_wannier90_make + " lib && "
+prebuildopts += "cd %(builddir)s/pyWannier90-*/src && "
+
+buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version
+# with Intel compilers, use libwannier90_intel as make target
+# with GCC compilers, use libwannier90_gf as make target
+buildopts += "libwannier90_gf && "
+buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py"""
+
+files_to_copy = [
+    (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import libwannier90'",
+    "python -c 'import pywannier90'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'chem'