From 2c9b28bc7e028d1225c709f81f6322a3e77c9c21 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 16:08:18 +0200 Subject: [PATCH 01/19] adding easyconfigs: CodingQuarry-2.0-foss-2023a.eb, DBD-mysql-4.050-GCC-12.3.0.eb, GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb, GlimmerHMM-3.0.4c-GCC-12.3.0.eb, Infernal-1.1.5-foss-2023a.eb, Jellyfish-2.3.1-GCC-12.3.0.eb, Proteinortho-6.3.2-gompi-2023a.eb, RSEM-1.3.3-foss-2023a-Java-11.eb, SNAP-HMM-20221022-GCC-12.3.0.eb, StringTie-2.2.3-GCC-12.3.0.eb, Trinity-2.15.1-foss-2023a.eb, eggnog-mapper-2.1.12-foss-2023a.eb, funannotate-1.8.17-foss-2023a.eb, tRNAscan-SE-2.0.12-foss-2023a.eb, tantan-50-GCC-12.3.0.eb --- .../CodingQuarry-2.0-foss-2023a.eb | 51 ++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb | 30 ++++++ .../eggnog-mapper-2.1.12-foss-2023a.eb | 56 +++++++++++ .../funannotate-1.8.17-foss-2023a.eb | 96 +++++++++++++++++++ .../GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb | 54 +++++++++++ .../GlimmerHMM-3.0.4c-GCC-12.3.0.eb | 57 +++++++++++ .../i/Infernal/Infernal-1.1.5-foss-2023a.eb | 39 ++++++++ .../j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb | 40 ++++++++ .../Proteinortho-6.3.2-gompi-2023a.eb | 34 +++++++ .../r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb | 55 +++++++++++ .../SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb | 45 +++++++++ .../s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb | 49 ++++++++++ .../t/Trinity/Trinity-2.15.1-foss-2023a.eb | 64 +++++++++++++ .../tRNAscan-SE-2.0.12-foss-2023a.eb | 42 ++++++++ .../t/tantan/tantan-50-GCC-12.3.0.eb | 26 +++++ 15 files changed, 738 insertions(+) create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb create mode 100644 easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb new file mode 100644 index 000000000000..4757b9125f24 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'CodingQuarry' +version = '2.0' + +homepage = 'https://sourceforge.net/p/codingquarry' +description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['CodingQuarry_v%(version)s.tar.gz'] +patches = ['CodingQuarry-2.0_python3.patch'] +checksums = [ + {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, + {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), + 'QuarryFiles', + 'TESTING', +] + +fix_python_shebang_for = [ + 'bin/CufflinksGTF_to_CodingQuarryGFF3.py', + 'QuarryFiles/scripts/*.py', +] + +sanity_check_paths = { + 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'], +} + +sanity_check_commands = [ + "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'", + "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING", + "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3", +] + +modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb new file mode 100644 index 000000000000..eec33081a4c8 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('MariaDB', '11.6.0'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb new file mode 100644 index 000000000000..4937c8bba74a --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.12' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b3c53fb0e606a5cfec75cbc84f7c215f57f43ce00d8e50f449513acdad76da73'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('HMMER', '3.4'), + ('DIAMOND', '2.1.8'), + ('prodigal', '2.6.3'), + ('wget', '1.24.5'), + ('MMseqs2', '14-7e284'), + ('XlsxWriter', '3.1.3'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb new file mode 100644 index 000000000000..af2d819eeb55 --- /dev/null +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'funannotate' +version = '1.8.17' + +homepage = 'https://funannotate.readthedocs.io' +description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work + with higher eukaryotes)""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# see also https://github.com/nextgenusfs/funannotate/blob/master/docs/dependencies.rst +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('GOATOOLS', '1.4.5'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('DBD-mysql', '4.050'), + ('CodingQuarry', '2.0'), + ('Trinity', '2.15.1'), + ('AUGUSTUS', '3.5.0'), + ('BamTools', '2.5.2'), + ('BEDTools', '2.31.0'), + ('BLAST+', '2.14.1'), # provides makeblastdb, tblastn + ('BLAT', '3.7'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('ETE', '3.1.3'), + ('Exonerate', '2.4.0'), + ('FASTA', '36.3.8i'), + ('GlimmerHMM', '3.0.4c'), + ('GMAP-GSNAP', '2023-04-20'), # provides gmap + ('GeneMark-ET', '4.72'), # provides gmes_petap.pl + ('HISAT2', '2.2.1'), + ('HMMER', '3.4'), # provides hmmscan, hmmsearch + ('kallisto', '0.51.1'), + ('MAFFT', '7.520', '-with-extensions'), + ('minimap2', '2.26'), + ('pigz', '2.8'), + ('Proteinortho', '6.3.2'), + ('Kent_tools', '468'), # provides pslCDnaFilter + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('SignalP', '6.0h', '-fast'), + ('SNAP-HMM', '20221022'), + ('StringTie', '2.2.3'), + ('tRNAscan-SE', '2.0.12'), + ('tantan', '50'), + ('trimAl', '1.4.1'), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), + ('BioPerl', '1.7.8'), + ('EVidenceModeler', '2.1.0'), +] + +#missin installations tRNAscan-SE/2.0.12-foss-2023a, tantan/40-foss-2023a + +use_pip = True + +exts_list = [ + ('distro', '1.9.0', { + 'checksums': ['2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['bdadfd7a5636383c1c40c26dab37c5908a77e8c4064adced84f1ba9e86187a04'], + 'preinstallopts': ( + """sed -i 's|REQUIRES_PYTHON = ">=3.6.0, <3.10"|REQUIRES_PYTHON = ">=3.6.0"|' setup.py && """ + """sed -i 's|"biopython<1.80",|"biopython",|' setup.py && """ + ) + }), +] + +sanity_check_paths = { + 'files': ['bin/funannotate'], + 'dirs': [], +} + +modextrapaths = { + 'GENEMARK_PATH': '$EBROOTGENEMARKMINET', +} + +sanity_check_commands = [ + "funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'", + "funannotate check --show-versions", +] + + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 000000000000..d21f30ba953c --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb new file mode 100644 index 000000000000..ad435033f815 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +dependencies = [ + ('Perl', '5.36.1'), +] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + (['train/*.pm'], 'lib/perl%(perlmajver)s'), + 'trained_dir', 'README', 'train/readme.train', +] + +fix_perl_shebang_for = ['bin/trainGlimmerHMM'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [ + "%(namelower)s -h", + r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'", +] + +modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb new file mode 100644 index 000000000000..7a89f4503ebb --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.5" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..b1a629f7f1ed --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.1' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb new file mode 100644 index 000000000000..4cd050e7d314 --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Proteinortho' +version = '6.3.2' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/'] +sources = ['proteinortho-v%(version)s.tar.gz'] +checksums = ['3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), +] + +skipsteps = ['configure'] + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "PREFIX=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'], + 'dirs': [], +} + +sanity_check_commands = ["proteinortho --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb new file mode 100644 index 000000000000..dbebc0f591d0 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://deweylab.github.io/RSEM/' +description = "RNA-Seq by Expectation-Maximization" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc', # v1.3.3.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('HISAT2', '2.2.1', '-Java-%(javaver)s'), + ('STAR', '2.7.11b'), + ('Bowtie2', '2.5.1'), + ('Bowtie', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb new file mode 100644 index 000000000000..06b3173938ef --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20221022' +_commit = '4ad1e95' + +homepage = 'https://korflab.github.io/' +description = """ +SNAP is a general purpose gene finding program suitable for both eukaryotic and +prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid +Parser. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-20190603_makefile_correction.patch'] +checksums = [ + {'20221022.tar.gz': 'a85726b7d4199da1b213b613057600012a392ef1aa20198f1d571fac55bf643f'}, + {'SNAP-HMM-20190603_makefile_correction.patch': 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655'}, +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +files_to_copy = [ + (['hmm-assembler.pl', 'zff2gff3.pl', 'fathom', 'forge', 'snap', 'Zoe/zoe-loop'], 'bin'), + 'DNA', + 'HMM', + 'Zoe', +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/forge', 'bin/zoe-loop'], + 'dirs': ['Zoe'], +} + +sanity_check_commands = [ + 'snap 2>&1 | grep "^usage:"', + 'zoe-loop | grep "^usage:"', +] + +modextrapaths = {'ZOE': 'Zoe'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..b8bf61dd6cf2 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.2.3' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f372640b70a8fde763712d2f0565aff71f5facdc2300c8af829fea94a05ff208'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libdeflate', '1.18'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('HTSlib', '1.18'), + ('Python', '3.11.3'), +] + +local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +buildopts = 'release ' + local_libs + +# the test script downloads some test data from the internet +runtest = 'test' +testopts = local_libs + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py3'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help', 'prepDE.py3 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb new file mode 100644 index 000000000000..6b10fd591551 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.5.1'), + ('GMAP-GSNAP', '2023-04-20'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.18'), + ('Jellyfish', '2.3.1'), + ('kallisto', '0.51.1'), + ('ncurses', '6.4'), + ('RSEM', '1.3.3'), + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11b'), + ('zlib', '1.2.13'), +] + +withsampledata = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb new file mode 100644 index 000000000000..a9c9fa5f5c4b --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'http://trna.ucsc.edu/tRNAscan-SE/' +description = """tRNAscan-SE is the most widely employed tool for identifying + and annotating tRNA genes in genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://trna.ucsc.edu/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] + +builddependencies = [ + # tRNAscan-SE's configure script really wants Autoconf 2.69 + ('Autoconf', '2.71', '', SYSTEM), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Infernal', '1.1.5'), +] + +parallel = 1 + +# tRNAscan-SE.conf sets the Infernal bin directory to be ours. +postinstallcmds = [ + "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", +] + +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/tRNAscan-SE', 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm'], + 'dirs': ['include'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb new file mode 100644 index 000000000000..c4a4ce67c25b --- /dev/null +++ b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tantan' +version = '50' + +homepage = 'https://gitlab.com/mcfrith/tantan' +description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/'] +sources = ['tantan-%(version)s.tar.gz'] +checksums = ['a239e9fb3c059ed9eb4c25a29b3c44a2ef1c1b492a9780874f429de7ae8b5407'] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/tantan'], + 'dirs': [], +} + +sanity_check_commands = ["tantan --help"] + +moduleclass = 'bio' From fdaf939bb7c537b8361483f6e47cf64c8934ea5c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 21:14:54 +0200 Subject: [PATCH 02/19] fix style --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index af2d819eeb55..22a735ac9af6 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -56,8 +56,6 @@ dependencies = [ ('EVidenceModeler', '2.1.0'), ] -#missin installations tRNAscan-SE/2.0.12-foss-2023a, tantan/40-foss-2023a - use_pip = True exts_list = [ From 3f541a45eed06c4e82c7c5ef2f4efd5e31089f54 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 18 Oct 2024 22:00:46 +0200 Subject: [PATCH 03/19] add missing checksums --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb | 1 + easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb index d21f30ba953c..c5247c1cf5a3 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb @@ -33,6 +33,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['gatk-%(version)s.zip'] +checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ ('Java', '11', '', SYSTEM), diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb index b1a629f7f1ed..82821a0cc38c 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] - +checksums = ['ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd'] parallel = 1 From 15ce961779249b3a64a0d95b40482806c977dfeb Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 18 Oct 2024 23:21:53 +0200 Subject: [PATCH 04/19] Remove wrong references to Java --- ...EM-1.3.3-foss-2023a-Java-11.eb => RSEM-1.3.3-foss-2023a.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/r/RSEM/{RSEM-1.3.3-foss-2023a-Java-11.eb => RSEM-1.3.3-foss-2023a.eb} (94%) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb similarity index 94% rename from easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb rename to easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb index dbebc0f591d0..c3170802211e 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a-Java-11.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb @@ -12,7 +12,6 @@ easyblock = 'ConfigureMake' name = 'RSEM' version = '1.3.3' -versionsuffix = '-Java-%(javaver)s' homepage = 'https://deweylab.github.io/RSEM/' description = "RNA-Seq by Expectation-Maximization" @@ -40,7 +39,7 @@ dependencies = [ ('Perl-bundle-CPAN', '5.36.1'), ('R', '4.3.2'), ('R-bundle-CRAN', '2023.12'), - ('HISAT2', '2.2.1', '-Java-%(javaver)s'), + ('HISAT2', '2.2.1'), ('STAR', '2.7.11b'), ('Bowtie2', '2.5.1'), ('Bowtie', '1.3.1'), From 9a016ef98b98c9b7071bd9d2c8b35b5b4e0f3612 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:24:18 +0200 Subject: [PATCH 05/19] change dependencies to resolve duplicates with different versions --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb index 6b10fd591551..688984aca599 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb @@ -35,7 +35,7 @@ builddependencies = [ # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile dependencies = [ ('Java', '11', '', SYSTEM), - ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), @@ -55,7 +55,7 @@ dependencies = [ ('RSEM', '1.3.3'), ('Salmon', '1.10.3'), ('SAMtools', '1.18'), - ('STAR', '2.7.11b'), + ('STAR', '2.7.11a'), ('zlib', '1.2.13'), ] From febfc467212019e5dd469ad14bc0193c7002a4dc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:26:43 +0200 Subject: [PATCH 06/19] change dependencies to resolve duplicates with different versions --- easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb index c3170802211e..559d54704d53 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb @@ -40,7 +40,7 @@ dependencies = [ ('R', '4.3.2'), ('R-bundle-CRAN', '2023.12'), ('HISAT2', '2.2.1'), - ('STAR', '2.7.11b'), + ('STAR', '2.7.11a'), ('Bowtie2', '2.5.1'), ('Bowtie', '1.3.1'), ] From fad9256dbe02611fa81f29d2f837a5bdc1b9f64f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:29:38 +0200 Subject: [PATCH 07/19] change dependencies to resolve duplicates with different versions --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb new file mode 100644 index 000000000000..a2838a996544 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.2' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.5.1'), + ('GMAP-GSNAP', '2023-04-20'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.18'), + ('Jellyfish', '2.3.1'), + ('kallisto', '0.51.1'), + ('ncurses', '6.4'), + ('RSEM', '1.3.3'), + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('zlib', '1.2.13'), +] + +withsampledata = True + +moduleclass = 'bio' From cfe83af7e98c4a2a1519eda158b8b52b9e35e184 Mon Sep 17 00:00:00 2001 From: lara Date: Sat, 19 Oct 2024 22:34:19 +0200 Subject: [PATCH 08/19] remove old version of Trinity --- .../t/Trinity/Trinity-2.15.1-foss-2023a.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb deleted file mode 100644 index 688984aca599..000000000000 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2023a.eb +++ /dev/null @@ -1,64 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -name = 'Trinity' -version = '2.15.1' - -homepage = 'https://trinityrnaseq.github.io' -description = """Trinity represents a novel method for the efficient and robust de novo reconstruction - of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, - Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] -sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] -patches = ['Trinity-%(version)s_fix-bamsifter.patch'] -checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, -] - -builddependencies = [ - ('Autotools', '20220317'), - ('CMake', '3.26.3'), -] - -# for reference, list of dependencies in the container image used upstream: -# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile -dependencies = [ - ('Java', '11', '', SYSTEM), - ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), - ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), - ('GATK', '4.3.0.0', '-Java-%(javaver)s'), - ('Perl', '5.36.1'), - ('Perl-bundle-CPAN', '5.36.1'), - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('BLAST+', '2.14.1'), - ('BLAT', '3.7'), - ('Bowtie', '1.3.1'), - ('Bowtie2', '2.5.1'), - ('GMAP-GSNAP', '2023-04-20'), - ('HISAT2', '2.2.1'), - ('HTSlib', '1.18'), - ('Jellyfish', '2.3.1'), - ('kallisto', '0.51.1'), - ('ncurses', '6.4'), - ('RSEM', '1.3.3'), - ('Salmon', '1.10.3'), - ('SAMtools', '1.18'), - ('STAR', '2.7.11a'), - ('zlib', '1.2.13'), -] - -withsampledata = True - -moduleclass = 'bio' From e1c227f47f987359105ac2746cef2257293638cf Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Sat, 19 Oct 2024 22:36:56 +0200 Subject: [PATCH 09/19] change Trinity version --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index 22a735ac9af6..0eeac174f28b 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -21,7 +21,7 @@ dependencies = [ ('tbl2asn', '20230713', '-linux64', SYSTEM), ('DBD-mysql', '4.050'), ('CodingQuarry', '2.0'), - ('Trinity', '2.15.1'), + ('Trinity', '2.15.2'), ('AUGUSTUS', '3.5.0'), ('BamTools', '2.5.2'), ('BEDTools', '2.31.0'), From 68ce4bb3296a90a4ab52355a83a09738d17d9801 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 11:19:23 +0200 Subject: [PATCH 10/19] inject right checksums and change patch file for Trinity --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 4 ++-- .../Trinity/Trinity-2.15.2_fix-bamsifter.patch | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index a2838a996544..8ed7523a32fe 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -22,8 +22,8 @@ source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch new file mode 100644 index 000000000000..508450dfb180 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -0,0 +1,17 @@ +Fix build of Trinity plugin bamsifter: +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) +--- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 ++++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 +@@ -2,8 +2,8 @@ + + cwd = $(shell pwd) + +-sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h +- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts ++sift_bam_max_cov: sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp + + + htslib/version.h : From b2e5c965f8970ef6b1b99078b6813dcffed16361 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 14:53:07 +0200 Subject: [PATCH 11/19] fix checksum --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 8ed7523a32fe..147daa157b6c 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.1_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] builddependencies = [ From 59c8a5fc96e7a4802d4389e9d3076ed223780ae0 Mon Sep 17 00:00:00 2001 From: lara Date: Sun, 20 Oct 2024 23:50:27 +0200 Subject: [PATCH 12/19] fix checksum --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 147daa157b6c..7529d7686726 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ - {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, + {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, ] From c10793a93f7516ea88755d0c65eefc0aa2b33d9e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 08:12:53 +0200 Subject: [PATCH 13/19] hopefully the patch and checksum drama ends with this one --- .../t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- .../t/Trinity/Trinity-2.15.2_fix-bamsifter.patch | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 7529d7686726..c14b372365cd 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.2_fix-bamsifter.patch': 'ad515743ed2d0913f1bf4bea1053164bb3f076a30526bb6b287524e2f0fd1103'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'bcb35c45ffd82d3da073c4f768719c1e74786ec7810e8311c141a4ebffd48053'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch index 508450dfb180..f82c4126b992 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -1,9 +1,10 @@ Fix build of Trinity plugin bamsifter: -* use external HTSlib from EasyBuild environment -* use compilation flags from environment -author: Alex Domingo (Vrije Universiteit Brussel) ---- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 -+++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 + 2 * use external HTSlib from EasyBuild environment + 3 * use compilation flags from environment + 4 author: Alex Domingo (Vrije Universiteit Brussel) +diff -ru trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile +--- trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile 2024-08-01 14:53:23.000000000 +0200 ++++ trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile 2024-10-21 07:50:10.911559350 +0200 @@ -2,8 +2,8 @@ cwd = $(shell pwd) @@ -11,7 +12,7 @@ author: Alex Domingo (Vrije Universiteit Brussel) -sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h - g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts +sift_bam_max_cov: sift_bam_max_cov.cpp -+ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp htslib/version.h : From dd66bb63d3e16bf2ec5a47da39aad9146b84f882 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 08:16:30 +0200 Subject: [PATCH 14/19] hopefully the patch and checksum drama ends with this one --- .../t/Trinity/Trinity-2.15.2_fix-bamsifter.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch index f82c4126b992..9e414a414f1a 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -1,7 +1,7 @@ Fix build of Trinity plugin bamsifter: - 2 * use external HTSlib from EasyBuild environment - 3 * use compilation flags from environment - 4 author: Alex Domingo (Vrije Universiteit Brussel) +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) diff -ru trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile --- trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile 2024-08-01 14:53:23.000000000 +0200 +++ trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile 2024-10-21 07:50:10.911559350 +0200 From 1359bc0ba1f6a5232fff16e2c32ddfad78d46eb7 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 21 Oct 2024 14:08:55 +0200 Subject: [PATCH 15/19] hopefully the patch and checksum drama ends with this one --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index c14b372365cd..8ecc76c588a3 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, - {'Trinity-2.15.2_fix-bamsifter.patch': 'bcb35c45ffd82d3da073c4f768719c1e74786ec7810e8311c141a4ebffd48053'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'f557a3d462218e27f3601ac07edd2bbafe5fdb088ab81f642e7025edfe3e48ef'}, ] builddependencies = [ From d73399982f11233bff15b4c994d39cd4ef2ee6ec Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 24 Oct 2024 16:41:31 +0200 Subject: [PATCH 16/19] get sources from github --- .../t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb index a9c9fa5f5c4b..107e7dbb9c9f 100644 --- a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb @@ -9,9 +9,9 @@ description = """tRNAscan-SE is the most widely employed tool for identifying toolchain = {'name': 'foss', 'version': '2023a'} -source_urls = ['http://trna.ucsc.edu/software/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] +source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61'] builddependencies = [ # tRNAscan-SE's configure script really wants Autoconf 2.69 From 45228482140e7ae954605dcd6432f33994126514 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 18:48:14 +0100 Subject: [PATCH 17/19] change tbl2asn version that is compatible with RPATH enabled builds see #21756 --- .../easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb index 0eeac174f28b..ed9d55804150 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -18,7 +18,7 @@ dependencies = [ ('matplotlib', '3.7.2'), ('scikit-learn', '1.3.1'), ('Seaborn', '0.13.2'), - ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('tbl2asn', '20230713'), ('DBD-mysql', '4.050'), ('CodingQuarry', '2.0'), ('Trinity', '2.15.2'), From 59142601bafbc8001aadce45f6813f4359b7b444 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 30 Oct 2024 11:27:01 +0100 Subject: [PATCH 18/19] include DB as it is no longer a dependency of Perl or Perl-bundle-CPAN --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 8ecc76c588a3..867969666e1f 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -40,6 +40,7 @@ dependencies = [ ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), ('Perl-bundle-CPAN', '5.36.1'), + ('DB', '18.1.40'), # for DB_File ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('BLAST+', '2.14.1'), From a39ea4028ef0d9a6cbbe14bf3a3e00e1f604bc85 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 5 Nov 2024 09:59:29 +0100 Subject: [PATCH 19/19] resolve style error --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb index 867969666e1f..7c85236b0a4f 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -40,7 +40,7 @@ dependencies = [ ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.36.1'), ('Perl-bundle-CPAN', '5.36.1'), - ('DB', '18.1.40'), # for DB_File + ('DB', '18.1.40'), # for DB_File ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('BLAST+', '2.14.1'),