From bf946d0207293a4dcfe24422d5cc3b39fe70446a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 7 Nov 2024 14:30:51 +0100
Subject: [PATCH] progress on #450 VEP

---
 450_VEP/DBD-mysql-4.050-GCC-12.3.0.eb | 30 +++++++++++++++++++++++
 450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb | 35 ---------------------------
 450_VEP/VEP-113.0-GCC-12.3.0.eb       |  4 +--
 3 files changed, 32 insertions(+), 37 deletions(-)
 create mode 100644 450_VEP/DBD-mysql-4.050-GCC-12.3.0.eb
 delete mode 100644 450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb

diff --git a/450_VEP/DBD-mysql-4.050-GCC-12.3.0.eb b/450_VEP/DBD-mysql-4.050-GCC-12.3.0.eb
new file mode 100644
index 00000000..eec33081
--- /dev/null
+++ b/450_VEP/DBD-mysql-4.050-GCC-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'PerlModule'
+
+name = 'DBD-mysql'
+version = '4.050'
+
+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 = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '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'
diff --git a/450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb b/450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb
deleted file mode 100644
index 5489bb7b..00000000
--- a/450_VEP/DBD-mysql-5.009-GCC-12.3.0.eb
+++ /dev/null
@@ -1,35 +0,0 @@
-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)
diff --git a/450_VEP/VEP-113.0-GCC-12.3.0.eb b/450_VEP/VEP-113.0-GCC-12.3.0.eb
index 74852e1e..0419059c 100644
--- a/450_VEP/VEP-113.0-GCC-12.3.0.eb
+++ b/450_VEP/VEP-113.0-GCC-12.3.0.eb
@@ -15,9 +15,9 @@ sources = ['%(version)s.tar.gz']
 checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.36.1'),
     ('Archive-Zip', '1.68'),
-    ('DBD-mysql', '4.050'),  # TODO
+    ('DBD-mysql', '4.050'),
     ('BioPerl', '1.7.8'),
     ('Bio-DB-HTS', '3.01'),
     # VEP requires Compress::Raw::Zlib >= 2.103