diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..02c4c54ce077 --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..3f1bbc6fe83a --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb new file mode 100644 index 000000000000..b5c3d27e3715 --- /dev/null +++ b/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 "', +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio'