{bio}[GCC/12.3.0,foss/2023a] BRAKER v3.0.8, spaln v3.0.6b

easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb

@@ -0,0 +1,55 @@
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
+easyblock = 'Tarball'
+
+name = 'BRAKER'
+version = '3.0.8'
+
+homepage = 'https://github.com/Gaius-Augustus/BRAKER'
+description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET
+ and AUGUSTUS in novel eukaryotic genomes."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f2623290c3007a3e42719a0bb2713bec7226db222bfef742895a9d5d0b4ee526']
+
+dependencies = [
+ ('Perl', '5.36.1'),
+ ('Python', '3.11.3'),
+ ('AUGUSTUS', '3.5.0'),
+ ('GeneMark-ET', '4.72'),
+ ('BamTools', '2.5.2'),
+ ('SAMtools', '1.18'),
+ ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM),
+ ('spaln', '3.0.6b'),
+ ('Exonerate', '2.4.0'),
+ ('BLAST+', '2.14.1'),
+ ('Biopython', '1.83'),
+ ('DIAMOND', '2.1.8'),
+ ('CDBtools', '0.99'),
+]
+
+fix_perl_shebang_for = ['scripts/*.pl']
+fix_python_shebang_for = ['scripts/*.py']
+
+sanity_check_paths = {
+ 'files': [
+ 'scripts/braker.pl',
+ 'scripts/compare_intervals_exact.pl',
+ 'scripts/compute_accuracies.sh',
+ 'scripts/compute_accuracies.sh',
+ 'scripts/filterGenemark.pl',
+ 'scripts/findGenesInIntrons.pl',
+ 'scripts/gatech_pmp2hints.pl',
+ 'scripts/sortGeneMark.py',
+ ],
+ 'dirs': ['docs', 'example'],
+}
+
+sanity_check_commands = ["braker.pl --help"]
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/spaln/spaln-3.0.6a-GCC-12.3.0.eb

@@ -0,0 +1,49 @@
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
+easyblock = 'ConfigureMake'
+
+name = 'spaln'
+version = '3.0.6a'
+
+homepage = 'https://github.com/ogotoh/spaln'
+description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps
+ and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h;
+# see also https://github.com/ogotoh/spaln/issues/56
+toolchainopts = {'optarch': False}
+
+source_urls = ['https://github.com/ogotoh/spaln/archive/']
+sources = ['ver.%(version)s.tar.gz']
+checksums = ['63c46589374e7c2b9a767ef3170504637cb2a57a05d0090a1a8bc6656cd3f254']
+
+dependencies = [
+ ('zlib', '1.2.13'),
+ ('Perl', '5.36.1'),
+]
+
+start_dir = 'src'
+
+# not a standard `configure` - does not accept standard `--prefix` option
+# see https://github.com/ogotoh/spaln/issues/74
+prefix_opt = '--exec_prefix='
+
+configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb"
+
+installopts = 'DESTDIR=%(installdir)s/'
+
+fix_perl_shebang_for = ['seqdb/*.pl']
+
+sanity_check_paths = {
+ 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']],
+ 'dirs': ['seqdb', 'table'],
+}
+
+sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"]
+modextrapaths = {
+ 'PATH': 'seqdb',
+ 'PERL5LIB': 'seqdb',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb

@@ -0,0 +1,49 @@
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
+easyblock = 'ConfigureMake'
+
+name = 'spaln'
+version = '3.0.6b'
+
+homepage = 'https://github.com/ogotoh/spaln'
+description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps
+ and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h;
+# see also https://github.com/ogotoh/spaln/issues/56
+toolchainopts = {'optarch': False}
+
+source_urls = ['https://github.com/ogotoh/spaln/archive/']
+sources = ['ver.%(version)s.tar.gz']
+checksums = ['8e496ef6d02696543f4a5e31922f464555eff9b8405da366587ba7bea27b4e76']
+
+dependencies = [
+ ('zlib', '1.2.13'),
+ ('Perl', '5.36.1'),
+]
+
+start_dir = 'src'
+
+# not a standard `configure` - does not accept standard `--prefix` option
+# see https://github.com/ogotoh/spaln/issues/74
+prefix_opt = '--exec_prefix='
+
+configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb"
+
+installopts = 'DESTDIR=%(installdir)s/'
+
+fix_perl_shebang_for = ['seqdb/*.pl']
+
+sanity_check_paths = {
+ 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']],
+ 'dirs': ['seqdb', 'table'],
+}
+
+sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"]
+modextrapaths = {
+ 'PATH': 'seqdb',
+ 'PERL5LIB': 'seqdb',
+}
+
+moduleclass = 'bio'