{bio}[GCCcore/12.3.0,foss/2023a] CheckM v1.0.18, DendroPy v4.5.2 w/ Python 2.7.18

easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb

@@ -0,0 +1,64 @@
+# Updated from previous config
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'CheckM'
+version = '1.0.18'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/Ecogenomics/CheckM'
+description = """CheckM provides a set of tools for assessing the quality of
+genomes recovered from isolates, single cells, or metagenomes."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [
+    'https://pypi.python.org/packages/source/c/checkm-genome',
+    'https://data.ace.uq.edu.au/public/CheckM_databases/',
+]
+sources = [
+    'checkm-genome-%(version)s.tar.gz',
+    {
+        'filename': 'checkm_data_2015_01_16.tar.gz',
+        'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s",
+    },
+]
+checksums = [
+    '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7',  # checkm-genome-1.0.18.tar.gz
+    '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c',  # checkm_data_2015_01_16.tar.gz
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('pplacer', '1.1.alpha19', '', SYSTEM),
+    ('prodigal', '2.6.3'),
+    ('HMMER', '3.4'),
+    ('SciPy-bundle', '2024.06', versionsuffix),
+    ('matplotlib', '2.2.5', versionsuffix),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('DendroPy', '4.5.2', versionsuffix),
+]
+
+download_dep_fail = True
+use_pip = True
+
+# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm
+postinstallcmds = [
+    "cp -a %(builddir)s/data %(installdir)s",
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "%(installdir)s/bin/checkm data setRoot %(installdir)s/data",
+]
+
+sanity_check_paths = {
+    'files': ['bin/checkm'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

@@ -0,0 +1,45 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2014 The Cyprus Institute
+# Authors::   Thekla Loizou <t.loizou@cyi.ac.cy>
+# License::   MIT/GPL
+# $Id$
+#
+##
+# Update: Petr Král (INUITS)
+easyblock = 'PythonPackage'
+
+name = 'DendroPy'
+version = '4.5.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://dendropy.org/'
+description = """A Python library for phylogenetics and phylogenetic computing: 
+reading, writing, simulation, processing and manipulation of phylogenetic trees 
+(phylogenies) and characters."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Python', '2.7.18')]
+
+download_dep_fail = True
+use_pip = True
+
+fix_python_shebang_for = ['bin/*.py']
+
+sanity_check_paths = {
+    'files': ['bin/sumlabels.py', 'bin/sumtrees.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["sumtrees.py --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'