diff --git a/config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb b/config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb new file mode 100644 index 0000000..f4e2e24 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '39.01' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = "BBMap short read aligner, and other bioinformatic tools." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6'] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), +] + +prebuildopts = "cd jni && " +buildopts = "-f makefile.linux" + +modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code. +""" +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'jni/libbbtoolsjni.so'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb b/config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb new file mode 100644 index 0000000..39e0647 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb @@ -0,0 +1,54 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: 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: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.14.1' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'] + +builddependencies = [ + ('cpio', '2.15'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LMDB', '0.9.31'), +] + +# remove line that prepends system paths to $PATH from configure script +preconfigopts = 'sed -i "s|^PATH=\\(.*\\)$|#PATH=\\1 |" %(start_dir)s/src/build-system/configure && ' +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb b/config/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb new file mode 100644 index 0000000..a8e5449 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb b/config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb new file mode 100644 index 0000000..ca0c28f --- /dev/null +++ b/config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +# # +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.6.1' + +homepage = 'https://dendropy.org/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['26fcbe1cb5831301e8f1f2e15a0563620f0b8e29e6d409dd6a2a7c957dd64c16'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.11.5'), +] + +fix_python_shebang_for = ['bin/*.py'] +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['sumtrees.py --help'] + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb b/config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb new file mode 100644 index 0000000..004a969 --- /dev/null +++ b/config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +start_dir = '%(name)s%(version_major)s%(version_minor)s' +files_to_copy = [ + (['bin/ux64/liblpsolve%(version_major)s%(version_minor)s.a', 'bin/ux64/liblpsolve%(version_major)s%(version_minor)s.so'], 'lib'), + (['../lp*.h'], 'include'), +] +cmds_map = [('.*', 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && sh ccc')] + +sanity_check_paths = { + 'files': ['lib/liblpsolve%(version_major)s%(version_minor)s.a', 'lib/liblpsolve%(version_major)s%(version_minor)s.so'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb b/config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb new file mode 100644 index 0000000..1e8a7c5 --- /dev/null +++ b/config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'miniprot' +version = '0.14' + +homepage = 'https://github.com/lh3/miniprot' +description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. +It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. +Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much +faster at the residue alignment step.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['c2b6f367c1607632400f49e80d6ace882c4d01eeef7e92c771df5529fb30232b'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +files_to_copy = [ + (['*.h', '%(name)s.1', 'test', 'tex'], 'lib'), + (['%(name)s'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb b/config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb new file mode 100644 index 0000000..75e4659 --- /dev/null +++ b/config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb @@ -0,0 +1,47 @@ +# # +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +# # + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ['%(name)s -h'] + +moduleclass = 'bio'