{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 #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-13.3.0.eb

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
index 9656cf8476..2ecc296bdf 100644
--- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
@@ -6,17 +6,18 @@ version = '1.68'
 homepage = 'https://metacpan.org/pod/Archive::Zip'
 description = "Provide an interface to ZIP archive files."
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
-sources = [SOURCE_TAR_GZ]
+sources = ['%(name)s-%(version)s.tar.gz']
 checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
 
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.40'),
 ]
+
 dependencies = [
-    ('Perl', '5.38.2'),
+    ('Perl', '5.36.1'),
     ('UnZip', '6.0'),
     ('Zip', '3.0'),
 ]

Diff against Archive-Zip-1.68-GCCcore-13.2.0.eb

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
index 389e96b3d0..2ecc296bdf 100644
--- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb
@@ -6,17 +6,18 @@ version = '1.68'
 homepage = 'https://metacpan.org/pod/Archive::Zip'
 description = "Provide an interface to ZIP archive files."
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
-sources = [SOURCE_TAR_GZ]
+sources = ['%(name)s-%(version)s.tar.gz']
 checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
 
 builddependencies = [
     ('binutils', '2.40'),
 ]
+
 dependencies = [
-    ('Perl', '5.38.0'),
+    ('Perl', '5.36.1'),
     ('UnZip', '6.0'),
     ('Zip', '3.0'),
 ]

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'),
 ]

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

Diff against Bio-DB-HTS-3.01-GCC-13.3.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb
index 490e86bfb7..1714b928bb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.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': '13.3.0'}
+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', '2.2.0')]
+builddependencies = [('pkgconf', '1.9.5')]
 
 dependencies = [
-    ('Perl', '5.38.2'),
+    ('Perl', '5.36.1'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.21'),
+    ('HTSlib', '1.18'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"

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"

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

Diff against Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
index 13ea1eaab8..d483a1964f 100644
--- a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb
@@ -6,19 +6,19 @@ 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': '13.3.0'}
+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 = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
 
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.38.2'),
-    ('zlib', '1.3.1'),
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
 ]
 
 options = {'modulename': 'Compress::Raw::Zlib'}

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 `VEP-113.0-GCC-12.3.0.eb`

Diff against VEP-113.3-GCC-13.3.0.eb

easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
index 1996303d91..fc4166c3cd 100644
--- a/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb
@@ -1,5 +1,5 @@
 name = 'VEP'
-version = '113.3'
+version = '113.0'
 
 homepage = 'https://www.ensembl.org/info/docs/tools/vep'
 description = """Variant Effect Predictor (VEP) determines the effect of your
@@ -8,16 +8,16 @@ 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': '13.3.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
 sources = ['%(version)s.tar.gz']
-checksums = ['ee68013eb035e17129e8f69977f525ebdd8321e73b3164a7bda6e103e2d10beb']
+checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164']
 
 dependencies = [
-    ('Perl', '5.38.2'),
+    ('Perl', '5.36.1'),
     ('Archive-Zip', '1.68'),
-    ('DBD-mysql', '4.051'),
+    ('DBD-mysql', '4.050'),
     ('BioPerl', '1.7.8'),
     ('Bio-DB-HTS', '3.01'),
     # VEP requires Compress::Raw::Zlib >= 2.103

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..fc4166c3cd 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
@@ -39,4 +39,6 @@ exts_list = [
     }),
 ]
 
+sanity_check_commands = ['vep --help']
+
 moduleclass = 'bio'

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..fc4166c3cd 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'", "")
 
@@ -35,4 +39,6 @@ exts_list = [
     }),
 ]
 
+sanity_check_commands = ['vep --help']
+
 moduleclass = 'bio'

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.

boegel · 2024-12-03T19:35:32Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3141.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/5f7a83267bc9bb3e31337d2ad2934f13 for a full test report.

…asyconfigs into 20241107143312_new_pr_VEP1130

easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb

boegel · 2024-12-10T16:20:43Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3102.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/9f41a557b71fbe31390ac7b7a56a8957 for a full test report.

boegel · 2024-12-10T16:43:27Z

Going in, thanks @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

PetrKralCZ added the update label Nov 7, 2024

PetrKralCZ mentioned this pull request Nov 7, 2024

VEP vscentrum/vsc-software-stack#450

Closed

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

boegel changed the title ~~{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, DBD-mysql v4.050, ...~~ {bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213, DBD-mysql v4.050 Dec 3, 2024

boegel added this to the 4.x milestone Dec 3, 2024

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

3fb1dfc

…asyconfigs into 20241107143312_new_pr_VEP1130

boegel changed the title ~~{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213, DBD-mysql v4.050~~ {bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 Dec 10, 2024

boegel requested changes Dec 10, 2024

View reviewed changes

easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb Show resolved Hide resolved

add custom sanity check command for VEP

c2a978b

boegel approved these changes Dec 10, 2024

View reviewed changes

boegel modified the milestones: 4.x, release after 4.9.4 Dec 10, 2024

boegel merged commit 5bd3238 into easybuilders:develop Dec 10, 2024
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{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 #21801

{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 #21801

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{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 #21801

{bio}[GCC/12.3.0] VEP v113.0, Archive-Zip v1.68, Bio-DB-HTS v3.01, Compress-Raw-Zlib v2.213 #21801

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PetrKralCZ commented Nov 7, 2024 • edited Loading

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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 VEP-113.0-GCC-12.3.0.eb

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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 `VEP-113.0-GCC-12.3.0.eb`

bedroge commented Nov 22, 2024 •

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