diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb new file mode 100644 index 00000000000..fa6a5add039 --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -0,0 +1,80 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähn +# uploaded by J. Sassmannshausen + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.10' + +homepage = 'https://cov-lineages.org/pangolin.html' +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Biopython', '1.78'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.18'), + ('Pysam', '0.16.0.1'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('UShER', '0.4.1'), + ('scikit-learn', '0.23.2'), + ('Kent_tools', '411'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + +exts_list = [ + ('pangolin', '3.1.11', { + 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], + }), + ('pangoLEARN', '2021-08-09', { + 'modulename': 'pangoLEARN', + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], + }), + ('scorpio', '0.3.12', { + 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], + }), + ('constellations', '0.0.13', { + 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], + }), + ('pango-designation', '1.2.59', { + 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], + }), +] + +local_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'pangolin -pv', + 'scorpio -v', +] + +moduleclass = 'bio'