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

PetrKralCZ · 2024-11-07T13:33:15Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#450

…-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

github-actions · 2024-11-07T13:33:57Z

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 · 2024-11-07T14:01:14Z

@boegelbot please test @ generoso

boegelbot · 2024-11-07T14:05:12Z

@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

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-07T14:14:41Z

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.

PetrKralCZ · 2024-11-07T14:18:45Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-07T14:20:10Z

@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

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-07T14:27:02Z

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 · 2024-11-07T14:50:36Z

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

PetrKralCZ · 2024-11-07T16:15:49Z

@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.

verdurin · 2024-11-11T09:31:39Z

Test report by @verdurin
FAILED
Build succeeded for 4 out of 5 (5 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/e59fcf1da338af67d695875127327a06 for a full test report.

verdurin · 2024-11-11T11:35:26Z


#   Failed test 'run - count up/downstream (default)'
#   at ./t/Runner.t line 534.
#          got: '2'
#     expected: '1'

#   Failed test 'run - count up/downstream (10000)'
#   at ./t/Runner.t line 551.
#          got: '3'
#     expected: '2'

#   Failed test 'run - count up/downstream (1000,2000)'
#   at ./t/Runner.t line 570.
#          got: '5'
#     expected: '4'
# Looks like you failed 3 tests of 110.
./t/Runner.t .........................................

verdurin · 2024-11-11T11:36:15Z

It's the same error I saw on Simon's slightly older version.

boegel · 2024-11-22T12:43:20Z

@bedroge @branfosj @smoors @akesandgren @bartoldeman Can you take this for a spin on your systems, and see if anyone else has the issue that @verdurin saw?

branfosj · 2024-11-22T12:48:18Z

@bedroge @branfosj @smoors @akesandgren @bartoldeman Can you take this for a spin on your systems, and see if anyone else has the issue that @verdurin saw?

Test reports on the way, but I think it'll be fine since #21772 built for me.

branfosj · 2024-11-22T12:53:22Z

Test report by @branfosj
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/711f6186d4f43d53cf0b9430efb89e05 for a full test report.

bedroge · 2024-11-22T12:53:55Z

Test report by @bedroge
FAILED
Build succeeded for 7 out of 9 (5 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/641230d2bc907f28441076791d78ac6a for a full test report.

bedroge · 2024-11-22T12:55:56Z

Test report by @bedroge FAILED Build succeeded for 7 out of 9 (5 easyconfigs in total) interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8 See https://gist.github.com/bedroge/641230d2bc907f28441076791d78ac6a for a full test report.

For me the Bio-DB-HTS tests are failing:

Test Summary Report
-------------------
t/01bam.t      (Wstat: 132 (Signal: ILL, dumped core) Tests: 0 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 452 tests but ran 0.
t/02faidx.t    (Wstat: 132 (Signal: ILL, dumped core) Tests: 4 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 15 tests but ran 4.
t/03cram.t     (Wstat: 132 (Signal: ILL, dumped core) Tests: 0 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 139 tests but ran 0.
t/04tabix.t    (Wstat: 132 (Signal: ILL, dumped core) Tests: 1 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 21 tests but ran 1.
t/05vcf.t      (Wstat: 132 (Signal: ILL, dumped core) Tests: 5 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 177 tests but ran 5.
t/07cramwrite.t (Wstat: 132 (Signal: ILL, dumped core) Tests: 0 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/08bamwrite.t (Wstat: 132 (Signal: ILL, dumped core) Tests: 0 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/09sam.t      (Wstat: 132 (Signal: ILL, dumped core) Tests: 0 Failed: 0)
  Non-zero wait status: 132
  Parse errors: No plan found in TAP output
t/10leak.t     (Wstat: 132 (Signal: ILL, dumped core) Tests: 3 Failed: 0)
  Non-zero wait status: 132
  Parse errors: Bad plan.  You planned 6 tests but ran 3.
Files=11, Tests=121,  4 wallclock secs ( 0.05 usr  0.05 sys +  1.29 cusr  0.93 csys =  2.32 CPU)
Result: FAIL
Failed 9/11 test programs. 0/121 subtests failed.

Edit: may be an issue with a conflicting HTSlib in my home directory, which was compiled for another microarchitecture. Let me try again...

branfosj · 2024-11-22T12:56:07Z

Test report by @branfosj
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/branfosj/a298d1d5de740ca909264617d3652026 for a full test report.

bedroge · 2024-11-22T13:23:08Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/5702ccb1924e3f44f36990a537377c2b for a full test report.

bedroge · 2024-11-22T13:55:19Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.1 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/be5af3b6811c97249d0850047d6a3ee3 for a full test report.

PetrKralCZ · 2024-11-25T14:23:09Z

@verdurin Can you run perl ensembl-vep/t/Runner.t to see more details about what went wrong?
You can also provide the result here directly: Ensembl/ensembl-vep#1802

smoors · 2024-11-25T18:51:33Z

Test report by @smoors
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node300.hydra.os - Linux Rocky Linux 8.10, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/smoors/414c8cefd9044ac4af9a8d1be77d6d93 for a full test report.

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

PetrKralCZ added the update label Nov 7, 2024

PetrKralCZ mentioned this pull request Nov 7, 2024

VEP vscentrum/vsc-software-stack#450

Open

9 tasks

branfosj mentioned this pull request Nov 11, 2024

{bio}[GCC/12.3.0] VEP v113, DBD-mysql v4.052, Bio-DB-HTS v3.01, ... #21772

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

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

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

PetrKralCZ commented Nov 7, 2024 •

edited

Loading

github-actions bot commented Nov 7, 2024

PetrKralCZ commented Nov 7, 2024

boegelbot commented Nov 7, 2024

boegelbot commented Nov 7, 2024

PetrKralCZ commented Nov 7, 2024

boegelbot commented Nov 7, 2024

boegelbot commented Nov 7, 2024

laraPPr commented Nov 7, 2024

PetrKralCZ commented Nov 7, 2024

verdurin commented Nov 11, 2024

verdurin commented Nov 11, 2024

verdurin commented Nov 11, 2024

boegel commented Nov 22, 2024

branfosj commented Nov 22, 2024

branfosj commented Nov 22, 2024

bedroge commented Nov 22, 2024

bedroge commented Nov 22, 2024 •

edited

Loading

branfosj commented Nov 22, 2024

bedroge commented Nov 22, 2024

bedroge commented Nov 22, 2024

PetrKralCZ commented Nov 25, 2024 •

edited

Loading

smoors commented Nov 25, 2024

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

Are you sure you want to change the base?

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

Conversation

PetrKralCZ commented Nov 7, 2024 • edited Loading

github-actions bot commented Nov 7, 2024

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

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

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

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

Updated software VEP-113.0-GCC-12.3.0.eb

PetrKralCZ commented Nov 7, 2024

boegelbot commented Nov 7, 2024

boegelbot commented Nov 7, 2024

PetrKralCZ commented Nov 7, 2024

boegelbot commented Nov 7, 2024

boegelbot commented Nov 7, 2024

laraPPr commented Nov 7, 2024

PetrKralCZ commented Nov 7, 2024

verdurin commented Nov 11, 2024

verdurin commented Nov 11, 2024

verdurin commented Nov 11, 2024

boegel commented Nov 22, 2024

branfosj commented Nov 22, 2024

branfosj commented Nov 22, 2024

bedroge commented Nov 22, 2024

bedroge commented Nov 22, 2024 • edited Loading

branfosj commented Nov 22, 2024

bedroge commented Nov 22, 2024

bedroge commented Nov 22, 2024

PetrKralCZ commented Nov 25, 2024 • edited Loading

smoors commented Nov 25, 2024

PetrKralCZ commented Nov 7, 2024 •

edited

Loading

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

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

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

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

Updated software `VEP-113.0-GCC-12.3.0.eb`

bedroge commented Nov 22, 2024 •

edited

Loading

PetrKralCZ commented Nov 25, 2024 •

edited

Loading