From f747dc2ffc473057659983667dd2596b262ec52a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 30 Oct 2024 13:49:57 +0100
Subject: [PATCH] adding easyconfigs:
 OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb,
 Statistics-R-0.34-foss-2023a.eb

---
 ...0.9.0-20240703-foss-2023a-Python-3.11.3.eb | 64 +++++++++++++++++++
 .../Statistics-R-0.34-foss-2023a.eb           | 28 ++++++++
 2 files changed, 92 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb
 create mode 100644 easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb
new file mode 100644
index 00000000000..0c101c27d2f
--- /dev/null
+++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb
@@ -0,0 +1,64 @@
+easyblock = 'MakeCp'
+
+name = 'OPERA-MS'
+local_commit = '026f9a5'
+version = '0.9.0-20240703'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/CSB5/OPERA-MS'
+description = """OPERA-MS is a hybrid metagenomic assembler which combines the
+ advantages of short and long-read technologies to provide high quality
+ assemblies, addressing issues of low contiguity for short-read only assemblies,
+ and low base-pair quality for long-read only assemblies."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/CSB5/OPERA-MS/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['72a3e16287dd1f2098adac41930d6a54779a033f5bf78c2659580afae5a7280c']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('Statistics-R', '0.34'),
+    ('Python', '3.11.3'),
+]
+
+buildopts = 'CFLAGS="$CFLAGS"'
+
+files_to_copy = [
+    'OPERA-MS.pl',
+    'bin',
+    'src_utils',
+    'tools_opera_ms',
+    (['OPERA-LG/bin'], 'OPERA-LG'),
+]
+
+postinstallcmds = [
+    "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS",
+    'chmod +x %(installdir)s/bin/OPERA-MS',
+    'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl',
+    '%(installdir)s/bin/OPERA-MS ' + ' '.join([
+        '--contig-file test_files/contigs.fasta',
+        '--short-read1 test_files/R1.fastq.gz',
+        '--short-read2 test_files/R2.fastq.gz',
+        '--long-read test_files/long_read.fastq',
+        '--no-ref-clustering',
+        '--out-dir $TMPDIR',
+    ]),
+]
+
+fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl']
+fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py']
+
+sanity_check_paths = {
+    'files': ['bin/OPERA-MS'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'OPERA-MS --help',
+    'OPERA-MS check-dependency',
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb
new file mode 100644
index 00000000000..7a351d75a26
--- /dev/null
+++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb
@@ -0,0 +1,28 @@
+easyblock = 'PerlModule'
+
+name = 'Statistics-R'
+version = '0.34'
+
+homepage = 'https://metacpan.org/pod/Statistics::R'
+description = "Perl interface with the R statistical program"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY']
+sources = [SOURCE_TAR_GZ]
+checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('R', '4.3.2'),
+]
+
+options = {'modulename': 'Statistics::R'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'],
+}
+
+moduleclass = 'data'