progress on #450 VEP

450_VEP/Archive-Zip-1.68-GCCcore-12.3.0.eb

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+easyblock = 'PerlModule'
+
+name = 'Archive-Zip'
+version = '1.68'
+
+homepage = 'https://metacpan.org/pod/Archive::Zip'
+description = "Provide an interface to ZIP archive files."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('UnZip', '6.0'),
+    ('Zip', '3.0'),
+]
+
+options = {'modulename': 'Archive::Zip'}
+
+sanity_check_paths = {
+    'files': ['bin/crc32'],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'],
+}
+
+moduleclass = 'tools'

450_VEP/Bio-DB-HTS-3.01-GCC-12.3.0.eb

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+easyblock = 'PerlModule'
+
+name = 'Bio-DB-HTS'
+version = '3.01'
+
+homepage = 'https://metacpan.org/release/Bio-DB-HTS'
+description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/']
+sources = ['Bio-DB-HTS-%(version)s.tar.gz']
+checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42']
+
+builddependencies = [('pkgconf', '1.9.5')]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('BioPerl', '1.7.8'),
+    ('HTSlib', '1.18'),
+]
+
+preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
+
+options = {'modulename': 'Bio::DB::HTS'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'],
+}
+
+moduleclass = 'bio'

450_VEP/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb

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+easyblock = 'PerlModule'
+
+name = 'Compress-Raw-Zlib'
+version = '2.213'
+
+homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib'
+description = "Low-Level Interface to zlib or zlib-ng compression library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+options = {'modulename': 'Compress::Raw::Zlib'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'PerlModule'
+
+name = 'DBD-mysql'
+version = '5.009'
+
+homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm'
+description = "Perl binding for MySQL"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN']
+sources = [SOURCE_TAR_GZ]
+checksums = ['8552d90dfddee9ef36e7a696da126ee1b42a1a00fbf2c6f3ce43ca2c63a5b952']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('MariaDB', '11.6.0'),
+    ('zlib', '1.2.13'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+options = {'modulename': 'DBD::mysql'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH],
+    'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH],
+}
+
+moduleclass = 'data'
+
+# TODO
+# == 2024-11-05 14:03:39,931 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " perl Makefile.PL PREFIX=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/DBD-mysql/5.009-GCC-12.3.0 " exited with exit code 2 and output:
+# Can't locate Devel/CheckLib.pm in @INC (you may need to install the Devel::CheckLib module) (@INC contains: /apps/gent/RHEL8/cascadelake-ib/software/Perl/5.36.1-GCCcore-12.3.0/lib/perl5/site_perl/5.36.1/x86_64-linux-thread-multi /apps/gent/RHEL8/cascadelake-ib/software/Perl/5.36.1-GCCcore-12.3.0/lib/perl5/site_perl/5.36.1 /apps/gent/RHEL8/cascadelake-ib/software/Perl/5.36.1-GCCcore-12.3.0/lib/perl5/5.36.1/x86_64-linux-thread-multi /apps/gent/RHEL8/cascadelake-ib/software/Perl/5.36.1-GCCcore-12.3.0/lib/perl5/5.36.1) at Makefile.PL line 13.
+# BEGIN failed--compilation aborted at Makefile.PL line 13.
+#  (at easybuild/easybuild-framework/easybuild/tools/run.py:695 in parse_cmd_output)

450_VEP/VEP-113.0-GCC-12.3.0.eb

@@ -0,0 +1,42 @@
+name = 'VEP'
+version = '113.0'
+
+homepage = 'https://www.ensembl.org/info/docs/tools/vep'
+description = """Variant Effect Predictor (VEP) determines the effect of your
+ variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,
+ transcripts, and protein sequence, as well as regulatory regions.
+ Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
+ used routines in VEP."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
+sources = ['%(version)s.tar.gz']
+checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('Archive-Zip', '1.68'),
+    ('DBD-mysql', '4.050'),  # TODO
+    ('BioPerl', '1.7.8'),
+    ('Bio-DB-HTS', '3.01'),
+    # VEP requires Compress::Raw::Zlib >= 2.103
+    ('Compress-Raw-Zlib', '2.202'),  # TODO
+]
+
+# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed
+# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504)
+species = 'cyprinus_carpio_carpio'
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perl -e 'require %(ext_name)s'", "")
+
+exts_list = [
+    ('Bio::EnsEMBL::XS', '2.3.2', {
+        'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'],
+    }),
+]
+
+moduleclass = 'bio'