{bio}[foss/2023a] Trinotate v4.0.2, TransDecoder v5.7.1, PyBioLib v1.1.2250

easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb

@@ -0,0 +1,54 @@
+easyblock = "PythonBundle"
+
+name = 'PyBioLib'
+version = '1.1.2250'
+
+homepage = 'https://biolib.com/'
+description = """PyBioLib is a Python package for running BioLib applications from Python
+scripts and the command line.
+BioLib is a library of biological data science applications. Applications on
+BioLib range from small bioinformatics utilities to state-of-the-art machine
+learning algorithms for predicting characteristics of biological molecules."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('poetry', '1.5.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Flask', '2.3.3'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('websocket_client', '1.8.0', {
+        'modulename': 'websocket',
+        'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'],
+    }),
+    ('docker', '7.1.0', {
+        'checksums': ['ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c'],
+    }),
+    ('PyJWT', '2.9.0', {
+        'modulename': 'jwt',
+        'source_tmpl': SOURCELOWER_TAR_GZ,
+        'checksums': ['7e1e5b56cc735432a7369cbfa0efe50fa113ebecdc04ae6922deba8b84582d0c'],
+    }),
+    ('gunicorn', '23.0.0', {
+        'checksums': ['f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec'],
+    }),
+    ('pybiolib', version, {
+        'modulename': 'biolib',
+        'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &",
+        'checksums': ['1a0fb4a0256bfa8345b881ac9697cf94a50bcab2caa9ad063689dfc0035fe5a2'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'Tarball'
+
+name = 'TransDecoder'
+version = '5.7.1'
+
+homepage = 'https://github.com/TransDecoder/TransDecoder/wiki'
+description = """TransDecoder identifies candidate coding regions within transcript sequences,
+ such as those generated by de novo RNA-Seq transcript assembly using Trinity,
+ or constructed based on RNA-Seq alignments to the genome using
+ Tophat and Cufflinks."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/']
+sources = ['TransDecoder-v%(version)s.tar.gz']
+checksums = ['41dd5e95f6ba946ff21340417d867e5e99f123b4035779b25d3cffd20b828a30']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('CD-HIT', '4.8.1'),
+]
+
+sanity_check_paths = {
+    'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'],
+    'dirs': ['PerlLib', 'sample_data', 'util'],
+}
+
+sanity_check_commands = []
+
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': 'PerlLib',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb

@@ -0,0 +1,55 @@
+easyblock = 'Tarball'
+name = 'Trinotate'
+version = '4.0.2'
+
+homepage = 'https://github.com/Trinotate/Trinotate/wiki'
+description = """Trinotate is a comprehensive annotation suite designed for automatic functional
+annotation of transcriptomes, particularly de novo assembled transcriptomes,
+from model or non-model organisms. Trinotate makes use of a number of different
+well referenced methods for functional annotation including homology search to
+known sequence data (BLAST+/SwissProt), protein domain identification
+(HMMER/PFAM), protein signal peptide and transmembrane domain prediction
+(signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg
+databases). All functional annotation data derived from the analysis of
+transcripts is integrated into a SQLite database which allows fast efficient
+searching for terms with specific qualities related to a desired scientific
+hypothesis or a means to create a whole annotation report for a transcriptome."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = '%(name)s'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(name)s-v%(version)s.tar.gz']
+checksums = ['2f633df2e05e5d22e19159aa147060be7884a057314cad3e6db91dba8910fad1']
+
+# # for reference, list of dependencies in the container image used upstream:
+# # https://github.com/Trinotate/Trinotate/blob/master/Docker/Dockerfile
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('Python', '3.11.3'),
+    ('Trinity', '2.15.2'),
+    ('BLAST+', '2.14.1'),
+    ('DIAMOND', '2.1.8'),
+    ('eggnog-mapper', '2.1.12'),
+    ('HMMER', '3.4'),
+    ('Infernal', '1.1.5'),
+    ('PyBioLib', '1.1.2250'),
+    ('SAMtools', '1.18'),
+    ('TransDecoder', '5.7.1'),
+]
+
+sanity_check_paths = {
+    'files': ['Trinotate', 'run_TrinotateWebserver.pl'],
+    'dirs': ['PerlLib', 'resources', 'testing', 'util'],
+}
+
+sanity_check_commands = [
+    'Trinotate --help 2>&1 | grep -q "Trinotate --db <sqlite.db>"',
+]
+
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': 'PerlLib',
+}
+
+moduleclass = 'bio'