add WIP easyconfigs for anvio (#280)

280_anvio/ETE-3.1.3-foss-2023a.eb

@@ -0,0 +1,38 @@
+easyblock = 'PythonPackage'
+
+name = 'ETE'
+version = '3.1.3'
+
+homepage = 'http://etetoolkit.org'
+description = """A Python framework for the analysis and visualization of trees"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://pypi.python.org/packages/source/e/ete3']
+sources = ['ete3-%(version)s.tar.gz']
+patches = ['ETE-3.1.2-foss-2021b_fix_binpath.patch']
+checksums = [
+    {'ete3-3.1.3.tar.gz': '06a3b7fa8ed90187b076a8dbbe5b1b62acee94201d3c6e822f55f449601ef6f2'},
+    {'ETE-3.1.2-foss-2021b_fix_binpath.patch': 'f71d1135e87e1035736f67b92ebcfebd2ae4d57e48f45e25c1a6144c60f11fbd'},
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('lxml', '4.9.2'),
+    ('PyQt5', '5.15.10'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+options = {'modulename': 'ete3'}
+
+sanity_check_paths = {
+    'files': ['bin/ete3'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

280_anvio/Pysam-0.22.0-GCC-12.3.0.eb

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+easyblock = 'PythonPackage'
+
+name = 'Pysam'
+version = '0.22.0'
+
+homepage = 'https://github.com/pysam-developers/pysam'
+description = """Pysam is a python module for reading and manipulating Samfiles.
+ It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/pysam-developers/pysam/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('ncurses', '6.4'),
+    ('cURL', '8.0.1'),
+    ('XZ', '5.4.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

280_anvio/anvio.eb

@@ -0,0 +1,95 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'anvio'
+version = '8'
+
+homepage = 'https://merenlab.org/software/anvio/'
+description = """An analysis and visualization platform for 'omics data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'merenlab'
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Pysam', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('matplotlib', '3.7.2'),
+    ('prodigal', '2.6.3-20230127'),
+    ('Biopython', '1.83'),
+    ('h5py', '3.9.0'),
+    ('HMMER', '3.4'),
+    ('networkx', '3.1'),
+    ('numba', '0.58.1'),
+    ('statsmodels', '0.14.1'),
+    ('snakemake', '8.4.2'),
+    ('ETE', '3.1.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('bottle', '0.12.25', {
+        'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'],
+    }),
+    ('colored', '2.2.4', {
+        'checksums': ['595e1dd7f3b472ea5f12af21d2fec8a2ea2cf8f9d93e67180197330b26df9b61'],
+    }),
+    ('Django', '5.0.1', {
+        'checksums': ['8c8659665bc6e3a44fefe1ab0a291e5a3fb3979f9a8230be29de975e57e8f854'],
+    }),
+    ('illumina-utils', '2.13', {
+        'checksums': ['e688ca221ea6178614073b72205fce7b4a54695237c7aa96713492ecd99bd56e'],
+    }),
+    ('mistune', '3.0.2', {
+        'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'],
+    }),
+    ('multiprocess', '0.70.16', {
+        'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'],
+    }),
+    ('Paste', '3.7.1', {
+        'checksums': ['6d07a8e1c7fa72b8cf403762a002f80d12c0384056956dd0a87cb9a3be64749a'],
+    }),
+    ('plotext', '5.2.8', {
+        'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'],
+    }),
+    ('pyani', '0.2.12', {
+        'checksums': ['4f56b217656f53416b333b69495a4ba8cde782e64e475e1481cb2213ce6b9388'],
+    }),
+    ('rich_argparse', '1.4.0', {
+        'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'],
+    }),
+    (name, version, {
+        # remove too strict requirements for Python packages anvio depends on
+        'preinstallopts': "sed -i -e 's/==/>=/g' -e 's/<=.*//g' requirements.txt && ",
+        'source_urls': ['https://github.com/merenlab/anvio/releases/download/v%(version)s/'],
+        'checksums': ['13da84d48d7266a8986815efb024772fa26ad1c8a951d42897c3a51e3d924feb'],
+    }),
+]
+
+local_binaries_list = [
+    'anvi-pan-genome',
+    'anvi-script-reformat-fasta',
+    'anvi-profile',
+    'anvi-help',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries_list],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'anvi-self-test --suite mini',
+    'anvi-pan-genome --help',
+    'anvi-script-reformat-fasta --help',
+    'anvi-profile --version',
+    'anvi-help --help',
+]
+
+moduleclass = 'bio'

280_anvio/prodigal-2.6.3-20230127-GCCcore-12.3.0.eb

@@ -0,0 +1,47 @@
+##
+# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia
+# Homepage: https://www.adelaide.edu.au/phoenix/
+#
+# Copyright::   adelaide.edu.au/phoenix
+# Authors::	Robert Qiao <[email protected]>, Exe Escobedo <[email protected]>
+# License::	GPL-v3.0
+#
+# Updated: Pavel Grochal (INUITS)
+#
+# Notes::
+##
+
+easyblock = 'MakeCp'
+
+name = 'prodigal'
+local_commit = 'c1e2d36'
+version = '2.6.3-20230127'
+
+homepage = 'https://github.com/hyattpd/Prodigal/'
+
+description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
+   is a microbial (bacterial and archaeal) gene finding program developed
+   at Oak Ridge National Laboratory and the University of Tennessee."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['5b4ac9f99038b143c62f4d86d3f77bc801f64daca04c26ba9789bf0a64904ac9']
+
+builddependencies = [('binutils', '2.40')]
+
+files_to_copy = [
+    (['prodigal'], 'bin'),
+    (['*.h'], 'include'),
+    (['LICENSE'], 'license'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/prodigal'],
+    'dirs': ['include', 'license'],
+}
+
+sanity_check_commands = ["prodigal -h"]
+
+moduleclass = 'bio'

280_anvio/statsmodels-0.14.1-gfbf-2023a.eb

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+easyblock = 'PythonBundle'
+
+name = 'statsmodels'
+version = '0.14.1'
+
+homepage = 'https://www.statsmodels.org/'
+description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models,
+and perform statistical tests."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('patsy', '0.5.6', {
+        'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'],
+    }),
+    (name, version, {
+        'checksums': ['2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6'],
+        'preinstallopts': """sed -i 's/name=DISTNAME/name=DISTNAME, version = "%(version)s"/g' setup.py && """,
+    }),
+]
+
+moduleclass = 'math'