Merge pull request #13733 from sassy-crick/20210813113839_new_pr_pang…

…olin3110

{bio}[foss/2020b} pangolin v3.1.10

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'