diff --git a/easyconfigs/c/Circos/Circos-0.69-8-GCCcore-11.3.0.eb b/easyconfigs/c/Circos/Circos-0.69-8-GCCcore-11.3.0.eb new file mode 100644 index 00000000..1a2e91f2 --- /dev/null +++ b/easyconfigs/c/Circos/Circos-0.69-8-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'Circos' +version = '0.69-8' + +homepage = 'https://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://%(namelower)s.ca/distribution/'] +sources = [SOURCELOWER_TGZ] +checksums = ['6946ab442bef6b1e97b28486dc44554cf7acf112654d7cf00b960e7dbc27f288'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Perl', '5.34.1'), + ('GD', '2.75'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +sanity_check_commands = [('perl', '-e "use %(name)s"')] + +modextrapaths = {'PERL5LIB': 'lib'} + +moduleclass = 'bio' diff --git a/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2022a.eb b/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2022a.eb new file mode 100644 index 00000000..bdcc8aeb --- /dev/null +++ b/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2022a.eb @@ -0,0 +1,51 @@ +# 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': '2022a'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = [] +dependencies = [ + ('Python', '3.10.4'), + ('Biopython', '1.79'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.1.0'), + ('prodigal', '2.6.3'), + ('wget', '1.21.3'), + ('MMseqs2', '14-7e284'), + ('XlsxWriter', '3.0.8'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +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/easyconfigs/m/MetaEuk/MetaEuk-6-a5d39d9-GCC-11.3.0.eb b/easyconfigs/m/MetaEuk/MetaEuk-6-a5d39d9-GCC-11.3.0.eb new file mode 100644 index 00000000..4def0fcb --- /dev/null +++ b/easyconfigs/m/MetaEuk/MetaEuk-6-a5d39d9-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = "6-a5d39d9" + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' diff --git a/easyconfigs/s/sourmash/sourmash-4.6.1-foss-2022a.eb b/easyconfigs/s/sourmash/sourmash-4.6.1-foss-2022a.eb new file mode 100644 index 00000000..6bd84834 --- /dev/null +++ b/easyconfigs/s/sourmash/sourmash-4.6.1-foss-2022a.eb @@ -0,0 +1,58 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'sourmash' +version = "4.6.1" + +homepage = "https://github.com/sourmash-bio/sourmash" +description = """Quickly search, compare, and analyze genomic and metagenomic data sets. sourmash is + a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs + for a variety of sequence comparisons.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +buildininstalldir = True +exts_list = [ + ('mmh3', '3.0.0', { + 'checksums': ['d1ec578c09a07d3518ec9be540b87546397fa3455de73c166fcce51eaa5c41c5'], + }), + ('deprecation', '2.0.6', { + 'checksums': ['68071e5ae7cd7e9da6c7dffd750922be4825c7c3a6780d29314076009cc39c35'], + }), + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('screed', '1.0.5', { + 'checksums': ['ad1b894aac81a8ad32fd587d37acb3fb4e575f6d828da73713038cc180098178'], + }), + ('cachetools', '4.0.0', { + 'checksums': ['9a52dd97a85f257f4e4127f15818e71a0c7899f121b34591fcc1173ea79a0198'], + }), + ('milksnake', '0.1.6', { + 'checksums': ['0198f8932b4e136c29c0d0d490ff1bac03f82c3a7b2ee6f666e3683b64314fd9'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/, orcid=.*/ },/g' pyproject.toml && ", + 'checksums': ['c8e6712632a4ff4322946a89c4b81e50f7ac06f878e043aba8fd9e1fa013819c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easyconfigs/s/starfish/starfish-1.1.0-foss-2022a.eb b/easyconfigs/s/starfish/starfish-1.1.0-foss-2022a.eb new file mode 100644 index 00000000..fd8c5ae6 --- /dev/null +++ b/easyconfigs/s/starfish/starfish-1.1.0-foss-2022a.eb @@ -0,0 +1,73 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'starfish' +version = '1.1.0' + +homepage = "https://github.com/egluckthaler/starfish" +description = """starfish is a modular toolkit for giant mobile element annotation. Built primarily for + annotating Starship elements in fungal genomes, it can be easily adapted to find any large mobile element (≥6kb) + that shares the same basic architecture as a fungal Starship or a bacterial integrative and conjugative element: + a "captain" gene with zero or more "cargo" genes downstream of its 3' end. It is particularly well suited + for annotating low-copy number elements in a content independent manner. +""" +citing = """Gluck-Thaler, E., & Vogan, A. A. (2024). + Systematic identification of cargo-carrying genetic elements reveals + new dimensions of eukaryotic diversity. Nucleic Acids Research, 2024-06 +""" +github_account = 'egluckthaler' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Perl', '5.34.1'), + ('Boost.MPI', '1.79.0'), + ('Cantera', '2.5.1'), + ('Circos', '0.69-8'), + ('sourmash', '4.6.1'), + ('eggnog-mapper', '2.1.12'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.16.1'), # differ from pinned 1.6, but mostly bug-fixes and reliability + ('MCL', '14.137'), + ('HMMER', '3.3.2'), + ('BLAST+', '2.13.0'), # no major API change compared to pinned 1.12 + ('minimap2', '2.24'), + ('MetaEuk', '6-a5d39d9'), # excplicit indication of commit, otherwise the exact same version 6 + ('MAFFT', '7.505', '-with-extensions'), + ('MMseqs2', '14-7e284'), + ('MUMmer', '4.0.0rc1'), +] +source_urls = ['https://github.com/%(github_account)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_updated-version-in-starfish-exe.patch', + ('%(name)s-%(version)s_added-utility-script-for-concatenating-annotate-outp.patch', 1), + '%(name)s-%(version)s_bug-fix.patch'] +checksums = [ + {'v1.1.0.tar.gz': '6f734403488d3cc1c2baae45aafdad204d682175556af2721234eab24f9bd49d'}, + {'starfish-1.1.0_updated-version-in-starfish-exe.patch': + 'c659b63f9f9cf8ecf8a121ce0ddc33750e3c78464452c367bf9ec145502fca65'}, + {'starfish-1.1.0_added-utility-script-for-concatenating-annotate-outp.patch': + '16a59d1da223a23c03fe0349894d6f230a0be9900e82b7160119aed141810afa'}, + {'starfish-1.1.0_bug-fix.patch': '49ff8f0c7e390888a332b7bf77eb2af6a96c08cb5bb9040b51253f97533e092a'}, +] + +skipsteps = ['configure', 'install'] + +local_pattern = r's|.*\(boost/.*\.hpp\).*|#include <\1>|' +local_opts = r' CC=g++ LFLAGS=\"-std=c++11 -I$EBROOTBOOST/include\" ' + +prebuildopts = "sed -i '5d' build.sh && chmod +x {build.sh,bin/*} && " +prebuildopts += "sed -i '%s' CNEFinder/qgrams.cc && " % local_pattern +prebuildopts += 'sed -i "s|Makefile|Makefile %s|" build.sh && ' % local_opts +prebuildopts += 'PREFIX=%(installdir)s SRC_DIR=%(start_dir)s ' +build_cmd = './build.sh' +buildopts = [' && chmod +x %(installdir)s/{aux/*,bin/cnef,bin/starfish}'] + +test_cmd = 'PATH="%(installdir)s/bin:$PATH" bash' +runtest = 'test.sh' +sanity_check_paths = { + 'files': ['bin/cnef'], + 'dirs': ['aux', 'main', 'lib', 'bin', 'db'] +} + +moduleclass = 'bio' diff --git a/easyconfigs/s/starfish/starfish-1.1.0_updated-version-in-starfish-exe.patch b/easyconfigs/s/starfish/starfish-1.1.0_updated-version-in-starfish-exe.patch new file mode 100644 index 00000000..114d7bc0 --- /dev/null +++ b/easyconfigs/s/starfish/starfish-1.1.0_updated-version-in-starfish-exe.patch @@ -0,0 +1,13 @@ +diff --git a/bin/starfish b/bin/starfish +index 86b3db1..053ed3e 100755 +--- a/bin/starfish ++++ b/bin/starfish +@@ -66,7 +66,7 @@ $starfishDIR\/db contains fastas and hmms of genes of interest, including YRs + } + + # Change software version here +-my $VERSION = "1.0.1"; ++my $VERSION = "1.1.0"; + + main: { +