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{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, DBD-mysql v4.050, ... #21801

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{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, DBD-mysql v4.050, ... #21801

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@PetrKralCZ PetrKralCZ commented Nov 7, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#450

@PetrKralCZ
adding easyconfigs: VEP-113.0-GCC-12.3.0.eb, Archive-Zip-1.68-GCCcore…
87fee92 
…-12.3.0.eb, DBD-mysql-4.050-GCC-12.3.0.eb, Bio-DB-HTS-3.01-GCC-12.3.0.eb, Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
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github-actions bot commented Nov 7, 2024

Updated software Archive-Zip-1.68-GCCcore-12.3.0.eb

Diff against Archive-Zip-1.68-GCCcore-12.2.0.eb

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
index 088d0a56de..2ecc296bdf 100644
--- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
@@ -6,18 +6,18 @@ version = '1.68'
 homepage = 'https://metacpan.org/pod/Archive::Zip'
 description = "Provide an interface to ZIP archive files."
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+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', '2.39'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.36.1'),
     ('UnZip', '6.0'),
     ('Zip', '3.0'),
 ]
Diff against Archive-Zip-1.68-GCCcore-11.3.0.eb

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
index ef7187f720..2ecc296bdf 100644
--- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
@@ -6,18 +6,18 @@ version = '1.68'
 homepage = 'https://metacpan.org/pod/Archive::Zip'
 description = "Provide an interface to ZIP archive files."
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+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', '2.38'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.36.1'),
     ('UnZip', '6.0'),
     ('Zip', '3.0'),
 ]
Diff against Archive-Zip-1.68-GCCcore-11.2.0.eb

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
index 6a2f22d453..2ecc296bdf 100644
--- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
@@ -6,18 +6,18 @@ version = '1.68'
 homepage = 'https://metacpan.org/pod/Archive::Zip'
 description = "Provide an interface to ZIP archive files."
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+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', '2.37'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.34.0'),
+    ('Perl', '5.36.1'),
     ('UnZip', '6.0'),
     ('Zip', '3.0'),
 ]

Updated software Bio-DB-HTS-3.01-GCC-12.3.0.eb

Diff against Bio-DB-HTS-3.01-GCC-12.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
index a3de8e7098..1714b928bb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
@@ -6,18 +6,18 @@ 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': '12.2.0'}
+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', '1.9.3')]
+builddependencies = [('pkgconf', '1.9.5')]
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.36.1'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.17'),
+    ('HTSlib', '1.18'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
Diff against Bio-DB-HTS-3.01-GCC-11.3.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
index 68542cd0da..1714b928bb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
@@ -6,18 +6,18 @@ 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': '11.3.0'}
+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', '1.8.0')]
+builddependencies = [('pkgconf', '1.9.5')]
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.36.1'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.15.1'),
+    ('HTSlib', '1.18'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
Diff against Bio-DB-HTS-3.01-GCC-11.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
index 87359ee843..1714b928bb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
@@ -6,18 +6,18 @@ 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': '11.2.0'}
+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', '1.8.0')]
+builddependencies = [('pkgconf', '1.9.5')]
 
 dependencies = [
-    ('Perl', '5.34.0'),
+    ('Perl', '5.36.1'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.14'),
+    ('HTSlib', '1.18'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"

Updated software Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb

Diff against Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb

easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
index c3c856455f..d483a1964f 100644
--- a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
@@ -1,24 +1,24 @@
 easyblock = 'PerlModule'
 
 name = 'Compress-Raw-Zlib'
-version = '2.202'
+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': '12.2.0'}
+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 = ['96e20946eb457a32d2d7a0050b922e37b5ada41246bcdc824196d3f7c4da91b7']
+checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
 
 builddependencies = [
-    ('binutils', '2.39'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.36.0'),
-    ('zlib', '1.2.12'),
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
 ]
 
 options = {'modulename': 'Compress::Raw::Zlib'}
Diff against Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb

easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
index a52e00e9f4..d483a1964f 100644
--- a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
@@ -1,24 +1,24 @@
 easyblock = 'PerlModule'
 
 name = 'Compress-Raw-Zlib'
-version = '2.202'
+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': '11.3.0'}
+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 = ['96e20946eb457a32d2d7a0050b922e37b5ada41246bcdc824196d3f7c4da91b7']
+checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
 
 builddependencies = [
-    ('binutils', '2.38'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.34.1'),
-    ('zlib', '1.2.12'),
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
 ]
 
 options = {'modulename': 'Compress::Raw::Zlib'}

Updated software DBD-mysql-4.050-GCC-12.3.0.eb

Diff against DBD-mysql-4.050-GCC-12.2.0.eb

easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
index 1cdd942d32..eec33081a4 100644
--- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
@@ -6,16 +6,17 @@ version = '4.050'
 homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm'
 description = "Perl binding for MySQL"
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+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', '5.36.0'),
-    ('MariaDB', '10.11.2'),
-    ('zlib', '1.2.12'),
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('MariaDB', '11.6.0'),
+    ('zlib', '1.2.13'),
     ('OpenSSL', '1.1', '', SYSTEM),
 ]
Diff against DBD-mysql-4.050-GCC-11.3.0.eb

easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
index 6d67a433eb..eec33081a4 100644
--- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
@@ -6,16 +6,17 @@ version = '4.050'
 homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm'
 description = "Perl binding for MySQL"
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+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', '5.34.1'),
-    ('MariaDB', '10.9.3'),
-    ('zlib', '1.2.12'),
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('MariaDB', '11.6.0'),
+    ('zlib', '1.2.13'),
     ('OpenSSL', '1.1', '', SYSTEM),
 ]
Diff against DBD-mysql-4.050-GCC-11.2.0.eb

easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
index 094f7bc25d..eec33081a4 100644
--- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb
@@ -6,16 +6,17 @@ version = '4.050'
 homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm'
 description = "Perl binding for MySQL"
 
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
+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', '5.34.0'),
-    ('MariaDB', '10.6.4'),
-    ('zlib', '1.2.11'),
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('MariaDB', '11.6.0'),
+    ('zlib', '1.2.13'),
     ('OpenSSL', '1.1', '', SYSTEM),
 ]

Updated software VEP-113.0-GCC-12.3.0.eb

Diff against VEP-111-GCC-12.2.0.eb

easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
index 3266a41274..0419059c6a 100644
--- a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
@@ -1,5 +1,5 @@
 name = 'VEP'
-version = '111'
+version = '113.0'
 
 homepage = 'https://www.ensembl.org/info/docs/tools/vep'
 description = """Variant Effect Predictor (VEP) determines the effect of your
@@ -8,20 +8,20 @@ description = """Variant Effect Predictor (VEP) determines the effect of your
  Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
  used routines in VEP."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
 sources = ['%(version)s.tar.gz']
-checksums = ['4e46a81640e8527e2717d6684fca13e6766fe7970c0410589195d77e19bd2971']
+checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.36.1'),
     ('Archive-Zip', '1.68'),
     ('DBD-mysql', '4.050'),
     ('BioPerl', '1.7.8'),
     ('Bio-DB-HTS', '3.01'),
     # VEP requires Compress::Raw::Zlib >= 2.103
-    ('Compress-Raw-Zlib', '2.202'),
+    ('Compress-Raw-Zlib', '2.213'),
 ]
 
 # To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed
Diff against VEP-107-GCC-11.3.0.eb

easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
index c6e1c1413c..0419059c6a 100644
--- a/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
@@ -1,5 +1,5 @@
 name = 'VEP'
-version = '107'
+version = '113.0'
 
 homepage = 'https://www.ensembl.org/info/docs/tools/vep'
 description = """Variant Effect Predictor (VEP) determines the effect of your
@@ -8,22 +8,26 @@ description = """Variant Effect Predictor (VEP) determines the effect of your
  Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
  used routines in VEP."""
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
 sources = ['%(version)s.tar.gz']
-checksums = ['4531acfe7a0dc3b1aaf0f9bead043cfb20b6df23a3a922a27a693dc532d0f741']
+checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.36.1'),
     ('Archive-Zip', '1.68'),
     ('DBD-mysql', '4.050'),
     ('BioPerl', '1.7.8'),
     ('Bio-DB-HTS', '3.01'),
     # VEP requires Compress::Raw::Zlib >= 2.103
-    ('Compress-Raw-Zlib', '2.202'),
+    ('Compress-Raw-Zlib', '2.213'),
 ]
 
+# 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'", "")
Diff against VEP-105-GCC-11.2.0.eb

easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
index 56b99eb9ac..0419059c6a 100644
--- a/easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
@@ -1,5 +1,5 @@
 name = 'VEP'
-version = '105'
+version = '113.0'
 
 homepage = 'https://www.ensembl.org/info/docs/tools/vep'
 description = """Variant Effect Predictor (VEP) determines the effect of your
@@ -8,27 +8,33 @@ description = """Variant Effect Predictor (VEP) determines the effect of your
  Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
  used routines in VEP."""
 
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
 sources = ['%(version)s.tar.gz']
-checksums = ['97ea8d3914b21b39ebd0504a71f3918f3d49d6d0266746b0295fe4f83754d81f']
+checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
 
 dependencies = [
-    ('Perl', '5.34.0'),
+    ('Perl', '5.36.1'),
     ('Archive-Zip', '1.68'),
     ('DBD-mysql', '4.050'),
     ('BioPerl', '1.7.8'),
     ('Bio-DB-HTS', '3.01'),
+    # VEP requires Compress::Raw::Zlib >= 2.103
+    ('Compress-Raw-Zlib', '2.213'),
 ]
 
+# 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 = ("perldoc -lm %(ext_name)s ", "")
+exts_filter = ("perl -e 'require %(ext_name)s'", "")
 
 exts_list = [
     ('Bio::EnsEMBL::XS', '2.3.2', {
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'],
+        'sources': ['%(version)s.tar.gz'],
         'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'],
     }),
 ]

@PetrKralCZ PetrKralCZ mentioned this pull request Nov 7, 2024
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@PetrKralCZ
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@boegelbot please test @ generoso

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@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21801 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21801 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14650

Test results coming soon (I hope)...

- notification for comment with ID 2462314335 processed

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it is of no use to you (unless you think I have a bug, which I don't).

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Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
cns2 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/7eee8fc9a862be512a53deeb010f1146 for a full test report.

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@boegelbot please test @ jsc-zen3

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@PetrKralCZ: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21801 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21801 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5216

Test results coming soon (I hope)...

- notification for comment with ID 2462355159 processed

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it is of no use to you (unless you think I have a bug, which I don't).

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Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/2ef7113fa4e4c1cea50048c3c4cdde9c for a full test report.

@laraPPr
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laraPPr commented Nov 7, 2024

@PetrKralCZ you are just using the DBD-mysql from this #21705 pr right? So that should not cause any conflicts?

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@PetrKralCZ you are just using the DBD-mysql from this #21705 pr right? So that should not cause any conflicts?

@laraPPr It is the exact easyconfig.

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VEP
3 participants
@PetrKralCZ @boegelbot @laraPPr