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{bio}[foss/2024a] OrthoFinder v3.1.0, replace the bundled famsa #26137

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{bio}[foss/2024a] OrthoFinder v3.1.0, replace the bundled famsa #26137

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cb1a800
replace the bundled famsa
wdlingit Jun 1, 2026
d30285e
added binutils and fixed hanging indent
wdlingit Jun 1, 2026
5e7b115
Update easybuild/easyconfigs/f/FAMSA/FAMSA-2.5.2-GCCcore-13.3.0.eb
wdlingit Jun 1, 2026
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43 changes: 43 additions & 0 deletions easybuild/easyconfigs/f/FAMSA/FAMSA-2.5.2-GCCcore-13.3.0.eb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
easyblock = 'MakeCp'

name = 'FAMSA'
version = '2.5.2'

homepage = 'https://github.com/refresh-bio/FAMSA'
description = """FAMSA2 is a progressive algorithm for large-scale multiple
sequence alignments"""

toolchain = {"name": "GCCcore", "version": "13.3.0"}

sources = [{
'filename': SOURCE_TAR_XZ,
'git_config': {
'url': 'https://github.com/refresh-bio',
'repo_name': 'FAMSA',
'commit': '2598410',
'clone_into': 'FAMSA-2.5.2',
},
}]
checksums = ['b00705aa660443b25421378a558defc05b2cf8a40657248348c372f469410335']

builddependencies = [
('binutils', '2.42'),
('CMake', '3.29.3'),
]

files_to_copy = [
(['bin/famsa'], 'bin'),
'LICENSE',
'README.md',
]

sanity_check_paths = {
'files': ['bin/famsa'],
'dirs': [],
}

sanity_check_commands = [
'famsa -h',
]

moduleclass = 'bio'
5 changes: 5 additions & 0 deletions easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-3.1.0-foss-2024a.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ dependencies = [
("BLAST+", "2.16.0"),
("DIAMOND", "2.1.11"),
("FastME", "2.1.6.3"),
("FAMSA", "2.5.2"),
("MCL", "22.282"),
("MMseqs2", "17-b804f"),
]
Expand Down Expand Up @@ -48,6 +49,10 @@ exts_list = [
),
]

postinstallcmds = [
'rm %(installdir)s/lib/python3.12/site-packages/orthofinder/bin/famsa',
]

sanity_check_paths = {
"files": [
"bin/orthofinder",
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