From 9697559d5660a0592eb2fbec6380c77ada2d7923 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 3 Mar 2025 11:04:55 +0100 Subject: [PATCH 1/4] adding easyconfigs: CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb, MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb, BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb --- ...EDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb | 55 +++++++++++++++++++ .../CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb | 51 +++++++++++++++++ ...AHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb | 40 ++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb new file mode 100644 index 000000000000..073ba7b0daba --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb @@ -0,0 +1,55 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Update: Petr Král (INUITS) + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec'] + +builddependencies = [ + ('Python', '2.7.18'), +] +dependencies = [ + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [ + 'bin', + 'docs', + 'data', + 'genomes', + 'scripts', + 'test', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb new file mode 100644 index 000000000000..e8b6076f54ed --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb new file mode 100644 index 000000000000..c821ab6263ed --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb @@ -0,0 +1,40 @@ +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': [], +} + +moduleclass = 'bio' From 54d709d1b7cd3c5d5b1d61795ecfafe7977791d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 3 Mar 2025 11:30:33 +0100 Subject: [PATCH 2/4] add sanity check commands --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb index c821ab6263ed..e2b057908f6d 100644 --- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb @@ -37,4 +37,10 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + + moduleclass = 'bio' From 5f098ef5e03c7170227da29cde5d55810d7ac30c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 3 Mar 2025 11:39:27 +0100 Subject: [PATCH 3/4] Update MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb delete empty line --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb index e2b057908f6d..85769e3a070b 100644 --- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb @@ -42,5 +42,4 @@ sanity_check_commands = [ "megahit --test", ] - moduleclass = 'bio' From 42122db2bbf2d6a3b9e333fb144bd3e56b436d14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 3 Mar 2025 17:24:23 +0100 Subject: [PATCH 4/4] remove unnecessary dependency --- ...EDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb deleted file mode 100644 index 073ba7b0daba..000000000000 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb +++ /dev/null @@ -1,55 +0,0 @@ -# Author: Maxime Schmitt, University of Luxembourg -# Author: Adam Huffman, The Francis Crick Institute -# -# Based on the work of: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel -# Update: Petr Král (INUITS) - -easyblock = 'MakeCp' - -name = 'BEDTools' -version = '2.31.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://bedtools.readthedocs.io/' -description = """BEDTools: a powerful toolset for genome arithmetic. -The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and -computing coverage. -The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec'] - -builddependencies = [ - ('Python', '2.7.18'), -] -dependencies = [ - ('XZ', '5.4.2'), - ('zlib', '1.2.13'), - ('bzip2', '1.0.8'), - ('BamTools', '2.5.2'), -] - -buildopts = 'CXX="$CXX"' - -files_to_copy = [ - 'bin', - 'docs', - 'data', - 'genomes', - 'scripts', - 'test', -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], - 'dirs': files_to_copy, -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'bio'