Merge pull request easybuilders#21861 from PetrKralCZ/20241115213220_…

…new_pr_bakta1100

{tools}[GCCcore/13.2.0] bakta v1.10.1, PyHMMER v0.10.15, psutil v6.1.0, ...

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/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/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'versioningit'
+version = '3.1.2'
+
+homepage = 'https://github.com/jwodder/versioningit'
+description = """versioningit is yet another Python packaging plugin for automatically determining your
+package’s version based on your version control repository’s tags.
+Unlike others, it allows easy customization of the version format and even lets you easily override
+the separate functions used for version extraction & calculation."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
+]
+dependencies = [('Python', '3.11.5')]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0']
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb

@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'zlib-ng'
+version = '2.2.2'
+
+homepage = 'https://github.com/zlib-ng/zlib-ng'
+description = """zlib data compression library for the next generation systems"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+    ('versioningit', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+components = [
+    (name, version, {
+        'easyblock': 'CMakeMake',
+        'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'],
+        'start_dir': '%(name)s-%(version)s',
+        'configopts': '-DZLIB_ENABLE_TESTS=ON',
+    }),
+
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, '0.5.1', {
+        'source_tmpl': 'zlib_ng-%(version)s.tar.gz',
+        'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'],
+        'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true',
+        'modulename': 'zlib_ng',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'