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

easybuild/easyconfigs/f/FAMSA/FAMSA-2.5.2-GCCcore-13.3.0.eb

@@ -0,0 +1,44 @@
+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': 'v2.5.2.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/refresh-bio',
+        'repo_name': 'FAMSA',
+        'commit': '2598410',
+        'clone_into': 'FAMSA-2.5.2',
+    },
+}]
+# check sum of the gz file
+checksums = ['751d97c64524a38f2e3ded8c50a3a297fbe1c2dff0b2685e4bcedcf66d85687b']
+
+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'

easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-3.1.0-foss-2024a.eb

@@ -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"),
 ]
@@ -48,6 +49,10 @@ exts_list = [
     ),
 ]
 
+postinstallcmds = [
+    'rm %(installdir)s/lib/python3.12/site-packages/orthofinder/bin/famsa',
+]
+
 sanity_check_paths = {
     "files": [
         "bin/orthofinder",