From fcbfc41867567735667185c33c058f8e1333fc8f Mon Sep 17 00:00:00 2001 From: Tony Kew Date: Wed, 12 Mar 2025 21:29:40 -0400 Subject: [PATCH] BUSCO version 5.8.3 easyconfig file Includes: AUGUSTUS version 3.5.0 BBMap version 39.01 BLAST+ version 2.14.1 BamTools version 2.5.2 DendroPy version 4.6.1 lpsolve version 5.5.2.11 MetaEuk version 7 miniprot version 0.14 prodigal version 2.6.3 SEPP version 4.5.5 Tony --- .../a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb | 79 +++++++++++++++++++ ...USTUS-3.5.0_sqliteDB_cstdint_include.patch | 43 ++++++++++ .../b/BBMap/BBMap-39.01-GCC-13.2.0.eb | 34 ++++++++ .../b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb | 56 +++++++++++++ .../b/BUSCO/BUSCO-5.8.3-foss-2023b.eb | 57 +++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb | 22 ++++++ .../DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb | 43 ++++++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb | 33 ++++++++ .../m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb | 31 ++++++++ .../miniprot/miniprot-0.14-GCCcore-13.2.0.eb | 33 ++++++++ .../prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb | 46 +++++++++++ .../s/SEPP/SEPP-4.5.5-foss-2023b.eb | 45 +++++++++++ 12 files changed, 522 insertions(+) create mode 100644 config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb create mode 100644 config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch create mode 100644 config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb create mode 100644 config/easybuild/easyconfigs/b/BUSCO/BUSCO-5.8.3-foss-2023b.eb create mode 100644 config/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb create mode 100644 config/easybuild/easyconfigs/s/SEPP/SEPP-4.5.5-foss-2023b.eb diff --git a/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb b/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb new file mode 100644 index 0000000..3813808 --- /dev/null +++ b/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb @@ -0,0 +1,79 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-3.5.0_sqliteDB_cstdint_include.patch'] +checksums = [ + '5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686', # v3.5.0.tar.gz + '1c5e1813f100531ec8a9fd0bc948612d37a5676eb8f5d59601ed2cfed65fa255', # AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch +] + +builddependencies = [ + ('Python', '3.11.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.83.0'), + ('GSL', '2.7'), + ('SAMtools', '1.19.2'), + ('HTSlib', '1.19.1'), # also provides tabix + ('BCFtools', '1.19'), + #('lpsolve', '5.6.20'), # lpsolve from r-bundle-cran + ('R-bundle-CRAN', '2024.06'), + ('SuiteSparse', '7.7.0', '-METIS-5.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.43.1'), + ('lpsolve', '5.5.2.11'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch b/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch new file mode 100644 index 0000000..0c914b4 --- /dev/null +++ b/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch @@ -0,0 +1,43 @@ +From 1ed97dc4ce2909c5f89737005b8ea4a664fbe728 Mon Sep 17 00:00:00 2001 +From: Kuoi +Date: Sun, 11 Jun 2023 23:47:49 +0800 +Subject: [PATCH] fix: gcc13 failed with this + +--- + include/sqliteDB.hh | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/include/sqliteDB.hh b/include/sqliteDB.hh +index e66374b9d..67a37826f 100644 +--- a/include/sqliteDB.hh ++++ b/include/sqliteDB.hh +@@ -11,6 +11,7 @@ + #include + #include + #include ++#include + + using namespace std; + +From 3dbe752e4cf3f6778168166a2c662d02d8623f15 Mon Sep 17 00:00:00 2001 +From: Kuoi +Date: Mon, 12 Jun 2023 01:32:02 +0800 +Subject: [PATCH] fix: without it compile fail + +--- + auxprogs/homGeneMapping/include/sqliteDB.hh | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/auxprogs/homGeneMapping/include/sqliteDB.hh b/auxprogs/homGeneMapping/include/sqliteDB.hh +index e842bcf9d..67338bef4 100644 +--- a/auxprogs/homGeneMapping/include/sqliteDB.hh ++++ b/auxprogs/homGeneMapping/include/sqliteDB.hh +@@ -13,6 +13,7 @@ + #include + #include + #include ++#include + + using namespace std; + + 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..aeef278 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb @@ -0,0 +1,34 @@ +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', '11.0.20', '', SYSTEM)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +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..aa35585 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb @@ -0,0 +1,56 @@ +# # +# 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 = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/b/BUSCO/BUSCO-5.8.3-foss-2023b.eb b/config/easybuild/easyconfigs/b/BUSCO/BUSCO-5.8.3-foss-2023b.eb new file mode 100644 index 0000000..4afbe49 --- /dev/null +++ b/config/easybuild/easyconfigs/b/BUSCO/BUSCO-5.8.3-foss-2023b.eb @@ -0,0 +1,57 @@ +# Updated by: Pavel Grochal (INUITS) +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.8.3' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b1a46c93b636ca59fd7529f8fba28774d9998c9a03d3f1fa8776a1fb08aa8b3f'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for pandas + ('R', '4.4.1'), # for R and ggplot2 + ('Biopython', '1.84'), + ('BLAST+', '2.14.1'), + ('HMMER', '3.4'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.5.0'), + ('SEPP', '4.5.5'), + ('MetaEuk', '7'), + ('BBMap', '39.01'), + ('miniprot', '0.14'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --cpu %(parallel)s --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --cpu %(parallel)s --mode geno --out test_eukaryota.out", +] + +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..89c7958 --- /dev/null +++ b/config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +## +# 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', '2.40')] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +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..03ed071 --- /dev/null +++ b/config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +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'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/config/easybuild/easyconfigs/m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb b/config/easybuild/easyconfigs/m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb new file mode 100644 index 0000000..62b8976 --- /dev/null +++ b/config/easybuild/easyconfigs/m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '7' +local_commit = 'bba0d80' + +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': '13.2.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['45eff3cb8e15626b1142d4717bf43a6e7a1308bc8a6eb1718c70d33d613898fa'] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' 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..445b2c1 --- /dev/null +++ b/config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +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/miniprot/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['c2b6f367c1607632400f49e80d6ace882c4d01eeef7e92c771df5529fb30232b'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('zlib', '1.2.13')] + +files_to_copy = [ + (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'), + (['miniprot'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/miniprot'], + '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..22a2163 --- /dev/null +++ b/config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +## +# 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', '2.40')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/config/easybuild/easyconfigs/s/SEPP/SEPP-4.5.5-foss-2023b.eb b/config/easybuild/easyconfigs/s/SEPP/SEPP-4.5.5-foss-2023b.eb new file mode 100644 index 0000000..0b95b3d --- /dev/null +++ b/config/easybuild/easyconfigs/s/SEPP/SEPP-4.5.5-foss-2023b.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.5' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v4.5.5.tar.gz': 'af6b985bc16c96cd7c57bf78b3decce448f976aea612b3fad07b91697e4e1cfd'}, + +] + +dependencies = [ + ('Python', '3.11.5'), + ('DendroPy', '4.6.1'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py'] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio'