{bio,tools}[foss/2025b,gompi/2025b] bakta v1.12.0, PyHMMER v0.12.0

easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb

@@ -0,0 +1,67 @@
+easyblock = 'PythonBundle'
+
+name = 'bakta'
+version = '1.12.0'
+
+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': '2025b'}
+
+builddependencies = [
+    ('scikit-build-core', '0.11.5'),
+    ('Cython', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Biopython', '1.86'),
+    ('PyYAML', '6.0.2'),
+    ('PyHMMER', '0.12.0'),
+    ('matplotlib', '3.10.5'),
+    ('python-isal', '1.7.0'),
+    ('python-zlib-ng', '0.5.1'),
+    ('archspec', '0.2.5'),
+]
+
+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', '3.7.0', {
+        'checksums': ['415940f07a9e6e60ca023b99381f2d5f62f801914b9edd6da5a28dd7307b091d'],
+    }),
+    ('xopen', '2.0.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
+    }),
+    (name, version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6772bc9defe423648a2e69976d91cb6ee109bf528aee01f235f4228e1a590b34'],
+    }),
+]
+
+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-0.12.0-gompi-2025b.eb

@@ -0,0 +1,43 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'PyHMMER'
+version = '0.12.0'
+
+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': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.1.2'),
+    ('scikit-build-core', '0.11.5'),
+]
+dependencies = [
+    ('Python', '3.13.5'),
+    ('HMMER', '3.4'),
+    ('psutil', '7.0.0'),
+]
+
+
+exts_list = [
+    ('pyhmmer', version, {
+        'patches': ['pyhmmer-disable-sabi-compat.patch'],
+        'preinstallopts': "export PYHMMER_FORCE_CYTHON=1 && ",
+        'checksums': [
+            {'pyhmmer-0.12.0.tar.gz': '27cdfd3cdf72abcc7a6670825fc0195e8ff01d4820efd0f99aec03d3972a922e'},
+            {'pyhmmer-disable-sabi-compat.patch': '972e4c2c31ab6ba564ea025b76afc8e5073194bbafa940c582aecd1f3ae81675'},
+        ],
+    }),
+]
+
+moduleclass = 'bio'