Merge pull request #22431 from PetrKralCZ/20250303110453_new_pr_CONCO…

…CT110

{bio}[GCC/12.3.0,GCCcore/12.3.0,foss/2023a] CONCOCT v1.1.0, MEGAHIT v1.2.9, BEDTools v2.31.0 w/ Python 2.7.18

easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb

@@ -0,0 +1,51 @@
+easyblock = 'PythonBundle'
+
+name = 'CONCOCT'
+version = '1.1.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://concoct.readthedocs.io'
+description = """Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a
+program for unsupervised binning of metagenomic contigs by using nucleotide
+composition, coverage data in multiple samples and linkage data from paired end
+reads."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('BEDTools', '2.31.0'),
+    ('Biopython', '1.76', versionsuffix),
+    ('Bowtie2', '2.5.4', versionsuffix),
+    ('CheckM', '1.0.18', versionsuffix),
+    ('GSL', '2.7'),
+    ('MEGAHIT', '1.2.9', versionsuffix),
+    ('parallel', '20230722'),
+    ('picard', '2.25.1', '-Java-11', SYSTEM),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('SAMtools', '1.18'),
+    ('scikit-learn', '0.20.4', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('nose', '1.3.7', {
+        'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/BinPro/CONCOCT/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/concoct'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["concoct --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb

@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'MEGAHIT'
+version = '1.2.9'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/voutcn/megahit'
+description = """An ultra-fast single-node solution for large and complex
+metagenomics assembly via succinct de Bruijn graph"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/voutcn/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('zlib', '1.2.13'),
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('bzip2', '1.0.8'),
+    ('gzip', '1.12'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/%(namelower)s',
+        'bin/%(namelower)s_core',
+        'bin/%(namelower)s_core_no_hw_accel',
+        'bin/%(namelower)s_core_popcnt',
+        'bin/%(namelower)s_toolkit',
+    ],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "megahit --version",
+    "megahit --test",
+]
+
+moduleclass = 'bio'