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..af469d2 --- /dev/null +++ b/config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb @@ -0,0 +1,78 @@ +# 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', '5.5.2.11'), + ('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/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/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/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' diff --git a/config/easybuild/easystacks/ccrsoft-2024.04-2023b-x86_64.yml b/config/easybuild/easystacks/ccrsoft-2024.04-2023b-x86_64.yml index b6e61fe..b653d41 100644 --- a/config/easybuild/easystacks/ccrsoft-2024.04-2023b-x86_64.yml +++ b/config/easybuild/easystacks/ccrsoft-2024.04-2023b-x86_64.yml @@ -24,3 +24,61 @@ easyconfigs: - code-server-4.90.2.eb - Julia-1.10.4-linux-x86_64.eb - scikit-learn-1.4.0-gfbf-2023b.eb + - BBMap-39.01-GCC-12.2.0.eb: + options: + try-toolchain-version: '13.2.0' + experimental: + try-update-deps: + copy-ec: + - BBMap-39.01-GCC-13.2.0.eb: + - BLAST+-2.14.1-gompi-2023a.eb: + options: + try-toolchain-version: '2023b' + experimental: + try-update-deps: + copy-ec: + - BLAST+-2.14.1-gompi-2023b.eb: + - BamTools-2.5.2-GCC-12.3.0.eb: + options: + try-toolchain-version: '13.2.0' + experimental: + try-update-deps: + copy-ec: + - BamTools-2.5.2-GCC-13.2.0.eb: + - DendroPy-4.6.1-GCCcore-12.3.0.eb: + options: + try-toolchain-version: '13.2.0' + experimental: + try-update-deps: + copy-ec: + - DendroPy-4.6.1-GCCcore-13.2.0.eb: + - lpsolve-5.5.2.11-GCC-12.2.0.eb: + options: + try-toolchain-version: '13.2.0' + experimental: + try-update-deps: + copy-ec: + - lpsolve-5.5.2.11-GCC-13.2.0.eb: + - AUGUSTUS-3.5.0-foss-2023b.eb: + - MetaEuk-7-GCC-13.2.0.eb: + - miniprot-0.13-GCCcore-12.3.0.eb: + options: + try-toolchain-version: '13.2.0' + try-software-version: '0.14' + experimental: + try-update-deps: + copy-ec: + - miniprot-0.14-GCCcore-13.2.0.eb: + options: + inject-checksums: 'sha256' + - miniprot-0.14-GCCcore-13.2.0.eb: + - prodigal-2.6.3-GCCcore-12.3.0.eb: + options: + try-toolchain-version: '13.2.0' + experimental: + try-update-deps: + copy-ec: + - prodigal-2.6.3-GCCcore-13.2.0.eb: + - SEPP-4.5.5-foss-2023b.eb: + - BUSCO-5.8.3-foss-2023b.eb: +