Merge pull request #22017 from pavelToman/20241212145119_new_pr_MitoF…

…inder142

{bio}[GCCcore/12.3.0,foss/2023a] MitoFinder v1.4.2, IDBA-UD v1.1.3 w/ Python 2.7.18

easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb

@@ -0,0 +1,51 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Updated: Pavel Grochal (INUITS)
+# License: GPLv2
+
+# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock
+# to be sure everything is copied and we run ./configure in prebuildopts
+
+# modified by Tom Strempel
+easyblock = 'MakeCp'
+
+name = 'IDBA-UD'
+version = '1.1.3'
+
+homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/'
+description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads
+Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm.
+IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth
+contigs are removed iteratively with cutoff threshold from low to high to reduce the errors
+in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled
+locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD
+can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
+to form long contigs in both low-depth and high-depth regions."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s']
+sources = ['idba-%(version)s.tar.gz']
+checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0']
+
+builddependencies = [('binutils', '2.40')]
+
+prebuildopts = './configure && '
+
+# we delete every .o and Makefile file which is left in bin folder
+buildopts = ' && rm -fr bin/*.o bin/Makefile*'
+
+files_to_copy = ["bin", "script", "ChangeLog", "NEWS"]
+
+pretestopts = "cd test && "
+runtest = "check"
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran",
+                                     "idba_ud", "parallel_blat", "idba_tran_test"]],
+    'dirs': [""],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb

@@ -0,0 +1,55 @@
+easyblock = 'Tarball'
+
+name = 'MitoFinder'
+version = '1.4.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/RemiAllio/MitoFinder'
+description = """MitoFinder is a pipeline to assemble mitochondrial genomes and
+annotate mitochondrial genes from trimmed read sequencing data"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/RemiAllio/MitoFinder/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['2d6d3925fb014777df97f272134143cc518944ae05d000a44ada2862d46ec95a']
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('Python', '2.7.18'),
+    ('IDBA-UD', '1.1.3'),
+    ('Infernal', '1.1.5'),
+    ('tRNAscan-SE', '2.0.12'),
+    ('Automake', '1.16.5'),
+]
+
+postinstallcmds = [
+    # avoid run install.sh + link EB modules
+    "rm -rf %(installdir)s/idba/bin && cd %(installdir)s/idba && ln -s $EBROOTIDBAMINUD/bin && "
+    "cd %(installdir)s/metaspades/bin && ln -s spades.py metaspades.py && "
+    "cd %(installdir)s/trnascanSE && mkdir -p infernal-1.1.3/exec && cd infernal-1.1.3/exec && "
+    "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && "
+    "cd %(installdir)s/trnascanSE && mkdir -p automake-1.13.4/exec && cd automake-1.13.4/exec && "
+    "ln -s $EBROOTAUTOMAKE/bin && ln -s $EBROOTAUTOMAKE/share && "
+    "cd %(installdir)s/trnascanSE && mkdir -p tRNAscan-SE-2.0/exec && cd tRNAscan-SE-2.0/exec && "
+    "ln -s $EBROOTTRNASCANMINSE/bin && ln -s $EBROOTTRNASCANMINSE/lib && ln -s $EBROOTTRNASCANMINSE/include && "
+    "cd %(installdir)s/mitfi && mkdir -p infernal-1.0.2/exec && cd infernal-1.0.2/exec && "
+    "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && "
+    "cd %(installdir)s/mitfi/infernal-1.0.2 && ln -s $EBROOTINFERNAL/bin src && "
+    'cd %(installdir)s && touch install.sh.ok && '
+    # fix mitofinder - https://github.com/RemiAllio/MitoFinder/issues/26
+    "sed -i 's/os.devnull, \'wb\')/os.devnull, \'wb\'), shell=True/g' mitofinder"
+]
+
+fix_python_shebang_for = ['mitofinder', '*.py']
+
+sanity_check_paths = {
+    'files': ['mitofinder'],
+    'dirs': ['idba', 'megahit', 'metaspades', 'mitfi', 'trnascanSE'],
+}
+
+sanity_check_commands = ['mitofinder -h']
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'