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{bio}[gompi/2023b] ABRicate v1.0.0, BLAST+ v2.16.0, BWA v0.7.18, ... w/ _saute.1.3.0_2 #22025

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merged 1 commit into from
Dec 18, 2024
Merged

{bio}[gompi/2023b] ABRicate v1.0.0, BLAST+ v2.16.0, BWA v0.7.18, ... w/ _saute.1.3.0_2 #22025

merged 1 commit into from
Dec 18, 2024

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akesandgren
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(created using eb --new-pr)

@akesandgren
adding easyconfigs: ABRicate-1.0.0-gompi-2023b.eb, BLAST+-2.16.0-gomp…
b37be0c 
…i-2023b.eb, BWA-0.7.18-GCCcore-13.2.0.eb, prokka-1.14.5-gompi-2023b.eb, SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb, VCFtools-0.1.16-GCC-13.2.0.eb
@github-actions GitHub Actions
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Updated software ABRicate-1.0.0-gompi-2023b.eb

Diff against ABRicate-1.0.0-gompi-2023a.eb

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb
index b21e8fda56..3e980962ec 100644
--- a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb
+++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb
@@ -9,7 +9,7 @@ version = '1.0.0'
 homepage = 'https://github.com/tseemann/abricate'
 description = "Mass screening of contigs for antimicrobial and virulence genes"
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 # https://github.com/tseemann/abricate
 github_account = 'tseemann'
@@ -18,10 +18,10 @@ sources = ['v%(version)s.zip']
 checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
 
 dependencies = [
-    ('Perl', '5.36.1'),
+    ('Perl', '5.38.0'),
     ('any2fasta', '0.4.2'),
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.14.1'),
+    ('BLAST+', '2.16.0'),
 ]
 
 postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']
Diff against ABRicate-1.0.0-gompi-2021a.eb

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb

diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb
index 097732fac3..3e980962ec 100644
--- a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb
+++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb
@@ -9,7 +9,7 @@ version = '1.0.0'
 homepage = 'https://github.com/tseemann/abricate'
 description = "Mass screening of contigs for antimicrobial and virulence genes"
 
-toolchain = {'name': 'gompi', 'version': '2021a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 # https://github.com/tseemann/abricate
 github_account = 'tseemann'
@@ -18,10 +18,10 @@ sources = ['v%(version)s.zip']
 checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
 
 dependencies = [
-    ('Perl', '5.32.1'),
+    ('Perl', '5.38.0'),
     ('any2fasta', '0.4.2'),
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.11.0'),
+    ('BLAST+', '2.16.0'),
 ]
 
 postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']

Updated software any2fasta-0.4.2-GCCcore-13.2.0.eb

Diff against any2fasta-0.4.2-GCCcore-12.3.0.eb

easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb
index 3f96b328b6..91034a25be 100644
--- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb
@@ -10,7 +10,7 @@ version = '0.4.2'
 homepage = 'https://github.com/tseemann/any2fasta'
 description = "Convert various sequence formats to FASTA"
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 # https://github.com/tseemann/any2fasta
 github_account = 'tseemann'
@@ -18,7 +18,7 @@ source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.zip']
 checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f']
 
-dependencies = [('Perl', '5.36.1')]
+dependencies = [('Perl', '5.38.0')]
 
 modextrapaths = {'PATH': ''}
Diff against any2fasta-0.4.2-GCCcore-11.2.0.eb

easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb
index 86bf9d1770..91034a25be 100644
--- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb
@@ -10,7 +10,7 @@ version = '0.4.2'
 homepage = 'https://github.com/tseemann/any2fasta'
 description = "Convert various sequence formats to FASTA"
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 # https://github.com/tseemann/any2fasta
 github_account = 'tseemann'
@@ -18,7 +18,7 @@ source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.zip']
 checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f']
 
-dependencies = [('Perl', '5.34.0')]
+dependencies = [('Perl', '5.38.0')]
 
 modextrapaths = {'PATH': ''}

Updated software BLAST+-2.16.0-gompi-2023b.eb

Diff against BLAST+-2.14.1-gompi-2023a.eb

easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb
index 844a985482..d43cb118ef 100644
--- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb
+++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb
@@ -13,31 +13,33 @@
 easyblock = 'ConfigureMake'
 
 name = 'BLAST+'
-version = '2.14.1'
+version = '2.16.0'
 
 homepage = 'https://blast.ncbi.nlm.nih.gov/'
 description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
  for comparing primary biological sequence information, such as the amino-acid
  sequences of different proteins or the nucleotides of DNA sequences."""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 toolchainopts = {'usempi': True, 'pic': True}
 
 source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/']
 sources = ['ncbi-blast-%(version)s+-src.tar.gz']
-checksums = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e']
+checksums = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b']
 
 builddependencies = [('cpio', '2.15')]
 
 dependencies = [
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
+    ('zstd', '1.5.5'),
     ('PCRE', '8.45'),
-    ('Boost', '1.82.0'),
-    ('GMP', '6.2.1'),
-    ('libpng', '1.6.39'),
-    ('libjpeg-turbo', '2.1.5.1'),
+    ('Boost', '1.83.0'),
+    ('GMP', '6.3.0'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
     ('LMDB', '0.9.31'),
+    ('SQLite', '3.43.1'),
 ]
 
 # remove line that prepends system paths to $PATH from configure script
Diff against BLAST+-2.14.0-gompi-2022b.eb

easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb
index a4033efcdd..d43cb118ef 100644
--- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb
+++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb
@@ -13,31 +13,33 @@
 easyblock = 'ConfigureMake'
 
 name = 'BLAST+'
-version = '2.14.0'
+version = '2.16.0'
 
 homepage = 'https://blast.ncbi.nlm.nih.gov/'
 description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
  for comparing primary biological sequence information, such as the amino-acid
  sequences of different proteins or the nucleotides of DNA sequences."""
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 toolchainopts = {'usempi': True, 'pic': True}
 
 source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/']
 sources = ['ncbi-blast-%(version)s+-src.tar.gz']
-checksums = ['bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500']
+checksums = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b']
 
 builddependencies = [('cpio', '2.15')]
 
 dependencies = [
-    ('zlib', '1.2.12'),
+    ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
+    ('zstd', '1.5.5'),
     ('PCRE', '8.45'),
-    ('Boost', '1.81.0'),
-    ('GMP', '6.2.1'),
-    ('libpng', '1.6.38'),
-    ('libjpeg-turbo', '2.1.4'),
-    ('LMDB', '0.9.29'),
+    ('Boost', '1.83.0'),
+    ('GMP', '6.3.0'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('LMDB', '0.9.31'),
+    ('SQLite', '3.43.1'),
 ]
 
 # remove line that prepends system paths to $PATH from configure script

Updated software BWA-0.7.18-GCCcore-13.2.0.eb

Diff against BWA-0.7.18-GCCcore-12.3.0.eb

easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb
index a5599e3764..d65b73e57e 100644
--- a/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb
@@ -29,7 +29,7 @@ description = """
  genome.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/lh3/%(name)s/archive/']
@@ -39,8 +39,8 @@ checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870']
 builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Perl', '5.36.1'),
     ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
 ]
 
 # Allow use of x86 intrinsics on PPC
Diff against BWA-0.7.17-20220923-GCCcore-12.3.0.eb

easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb
index 6f701c63b8..d65b73e57e 100644
--- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb
@@ -14,11 +14,13 @@
 # The Francis Crick Institute
 #
 # Note that upstream development is mainly at: https://github.com/lh3/bwa
+#
+# 0.7.18
+# Erica Bianco (HPCNow!)
 ##
 
 name = 'BWA'
-local_commit = '139f68f'
-version = '0.7.17-20220923'
+version = '0.7.18'
 
 homepage = 'http://bio-bwa.sourceforge.net/'
 description = """
@@ -27,18 +29,18 @@ description = """
  genome.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://github.com/lh3/bwa/archive']
-sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
-checksums = ['be460d6e13ddf34896aafae00bad71e05a0b9f7e23490eeeca8ad257065f5e60']
+source_urls = ['https://github.com/lh3/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870']
 
 builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Perl', '5.36.1'),
     ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
 ]
 
 # Allow use of x86 intrinsics on PPC

Updated software Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb

Diff against Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb

easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb
index d21b8fbf38..b26850e9d3 100644
--- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb
@@ -7,14 +7,14 @@ homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3'
 description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible
 with both version 2 and version 3 of the HMMER package from http://hmmer.org."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
 source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
 sources = [SOURCE_TAR_GZ]
 checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246']
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.38.0'),
     ('BioPerl', '1.7.8'),
 ]
Diff against Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb

easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb
index 840b2a8d6f..b26850e9d3 100644
--- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb
@@ -7,14 +7,14 @@ homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3'
 description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible
 with both version 2 and version 3 of the HMMER package from http://hmmer.org."""
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
 source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
 sources = [SOURCE_TAR_GZ]
 checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246']
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.38.0'),
     ('BioPerl', '1.7.8'),
 ]

Updated software prokka-1.14.5-gompi-2023b.eb

Diff against prokka-1.14.5-gompi-2022b.eb

easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb
index 94b4e5939e..bd7648a541 100644
--- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb
@@ -13,7 +13,7 @@ version = '1.14.5'
 homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml'
 description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes."
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = ['https://github.com/tseemann/prokka/archive/']
 sources = ['v%(version)s.zip']
@@ -21,11 +21,11 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
 
 dependencies = [
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.14.0'),
+    ('BLAST+', '2.16.0'),
     ('Java', '11', '', SYSTEM),
     ('Bio-SearchIO-hmmer', '1.7.3'),
-    ('parallel', '20230722'),
-    ('tbl2asn', '20230713', '-linux64', SYSTEM),
+    ('parallel', '20240322'),
+    ('tbl2asn', '20230713'),
 ]
 
 local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
Diff against prokka-1.14.5-gompi-2022a.eb

easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb
index c1a3cfa1cd..bd7648a541 100644
--- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb
@@ -13,7 +13,7 @@ version = '1.14.5'
 homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml'
 description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes."
 
-toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = ['https://github.com/tseemann/prokka/archive/']
 sources = ['v%(version)s.zip']
@@ -21,11 +21,11 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
 
 dependencies = [
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.13.0'),
+    ('BLAST+', '2.16.0'),
     ('Java', '11', '', SYSTEM),
     ('Bio-SearchIO-hmmer', '1.7.3'),
-    ('parallel', '20220722'),
-    ('tbl2asn', '20220427', '-linux64', SYSTEM),
+    ('parallel', '20240322'),
+    ('tbl2asn', '20230713'),
 ]
 
 local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',

Updated software SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb

Diff against SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb

easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb

diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb
index ebf4e97faf..5baecf1ad1 100644
--- a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb
+++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb
@@ -2,28 +2,28 @@ easyblock = 'MakeCp'
 
 name = 'SKESA'
 version = '2.4.0'
-versionsuffix = '_saute.1.3.0_1'
+versionsuffix = '_saute.1.3.0_2'
 
 homepage = 'https://github.com/ncbi/SKESA'
 description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs."
 
-toolchain = {'name': 'gompi', 'version': '2021b'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 toolchainopts = {'cstd': 'c++11'}
 
 source_urls = ['https://github.com/ncbi/SKESA/archive/']
 sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['b44c56b16d87b1961e9ee4069468f6b0e850c0cc4c99410f1f5c06b782dee092']
+checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979']
 
 dependencies = [
-    ('NGS', '2.11.2'),
-    ('ncbi-vdb', '2.11.2'),
-    ('Boost', '1.77.0'),
+    ('Boost', '1.83.0'),
+    ('SRA-Toolkit', '3.1.1'),
+    ('ncbi-vdb', '3.1.1'),
 ]
 
 prebuildopts = "touch %(builddir)s/ngs.done && "
 
 buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" '
-buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTNGS VDB_PATH=$EBROOTNCBIMINVDB"
+buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB"
 
 files_to_copy = [(['skesa'], 'bin')]
Diff against SKESA-2.3.0-foss-2018b.eb

easybuild/easyconfigs/s/SKESA/SKESA-2.3.0-foss-2018b.eb

diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.3.0-foss-2018b.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb
index da15e72a04..5baecf1ad1 100644
--- a/easybuild/easyconfigs/s/SKESA/SKESA-2.3.0-foss-2018b.eb
+++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb
@@ -1,28 +1,29 @@
 easyblock = 'MakeCp'
 
 name = 'SKESA'
-version = '2.3.0'
+version = '2.4.0'
+versionsuffix = '_saute.1.3.0_2'
 
 homepage = 'https://github.com/ncbi/SKESA'
 description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs."
 
-toolchain = {'name': 'foss', 'version': '2018b'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 toolchainopts = {'cstd': 'c++11'}
 
 source_urls = ['https://github.com/ncbi/SKESA/archive/']
-sources = ['v%(version)s.tar.gz']
-checksums = ['13832e41b69a94d9f64dee7685b4d05f2e94f807ad819afa8d4cd78cee54879d']
+sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz']
+checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979']
 
 dependencies = [
-    ('NGS', '2.9.3', '-Java-1.8'),
-    ('ncbi-vdb', '2.9.3'),
-    ('Boost', '1.67.0'),
+    ('Boost', '1.83.0'),
+    ('SRA-Toolkit', '3.1.1'),
+    ('ncbi-vdb', '3.1.1'),
 ]
 
 prebuildopts = "touch %(builddir)s/ngs.done && "
 
 buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" '
-buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTNGS VDB_PATH=$EBROOTNCBIMINVDB"
+buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB"
 
 files_to_copy = [(['skesa'], 'bin')]
 
@@ -31,4 +32,6 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = ["skesa --help"]
+
 moduleclass = 'bio'

Updated software tbl2asn-20230713-GCCcore-13.2.0.eb

Diff against tbl2asn-20230713-GCCcore-13.3.0.eb

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb
index 12b79ddde0..3571e61aac 100644
--- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb
@@ -13,12 +13,17 @@ homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
 description = """Tbl2asn is a command-line program that automates the creation of
  sequence records for submission to GenBank"""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.40'),
     ('patchelf', '0.18.0'),
 ]
 
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
 # libraries that are copied to installdir need to be patched to have an RPATH section
 # when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);
Diff against tbl2asn-20230713-GCCcore-12.3.0.eb

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb
index dcf4c39e8d..3571e61aac 100644
--- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb
@@ -13,12 +13,17 @@ homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
 description = """Tbl2asn is a command-line program that automates the creation of
  sequence records for submission to GenBank"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
 builddependencies = [
     ('binutils', '2.40'),
     ('patchelf', '0.18.0'),
 ]
 
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
 # libraries that are copied to installdir need to be patched to have an RPATH section
 # when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);

Updated software VCFtools-0.1.16-GCC-13.2.0.eb

Diff against VCFtools-0.1.16-GCC-12.3.0.eb

easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb
index 3cdfda35e1..3a4edc7bc1 100644
--- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb
@@ -8,19 +8,21 @@ description = """The aim of VCFtools is to provide
  easily accessible methods for working with complex 
  genetic variation data in the form of VCF files."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
-source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/']
+github_account = '%(namelower)s'
+source_urls = [GITHUB_LOWER_RELEASE]
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3']
 
 builddependencies = [
-    ('pkgconf', '1.9.5'),
+    ('pkgconf', '2.0.3'),
 ]
+
 dependencies = [
-    ('Perl', '5.36.1'),
-    ('HTSlib', '1.18'),
     ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+    ('HTSlib', '1.19.1'),
 ]
Diff against VCFtools-0.1.16-GCC-12.2.0.eb

easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb
index 0ff539325e..3a4edc7bc1 100644
--- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb
@@ -3,32 +3,34 @@ easyblock = 'ConfigureMake'
 name = 'VCFtools'
 version = '0.1.16'
 
-homepage = "https://vcftools.github.io"
+homepage = 'https://vcftools.github.io'
 description = """The aim of VCFtools is to provide 
  easily accessible methods for working with complex 
  genetic variation data in the form of VCF files."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
-source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/']
-sources = ['%(namelower)s-%(version)s.tar.gz']
+github_account = '%(namelower)s'
+source_urls = [GITHUB_LOWER_RELEASE]
+sources = [SOURCELOWER_TAR_GZ]
 checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3']
 
 builddependencies = [
-    ('pkgconf', '1.9.3'),
+    ('pkgconf', '2.0.3'),
 ]
 
 dependencies = [
-    ('Perl', '5.36.0'),
-    ('HTSlib', '1.17'),
-    ('zlib', '1.2.12'),
+    ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+    ('HTSlib', '1.19.1'),
 ]
 
-modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'}
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']],
+    'files': ['bin/%(namelower)s', 'bin/vcf-sort', 'bin/vcf-stats'],
     'dirs': [],
 }
 
+modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'}
+
 moduleclass = 'bio'

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@boegelbot Please test @ jsc-zen3

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@akesandgren: 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=22025 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22025 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5437

Test results coming soon (I hope)...

- notification for comment with ID 2542105795 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/7a1ace0441bcc2096be4c77b49fbc345 for a full test report.

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Test report by @verdurin
SUCCESS
Build succeeded for 20 out of 20 (9 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/2156e68d9d2e7e10787c7f8a4276df0f for a full test report.

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@boegelbot please test @ generoso

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

PR test command 'EB_PR=22025 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22025 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14877

Test results coming soon (I hope)...

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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 9 out of 9 (9 easyconfigs in total)
cns1 - 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/e4aea61b47c87f79a197610ddeaaad1a for a full test report.

@verdurin verdurin added this to the release after 4.9.4 milestone Dec 18, 2024
verdurin
verdurin approved these changes Dec 18, 2024
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Looks fine.

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Going in, thanks @akesandgren!

@verdurin verdurin merged commit b502436 into easybuilders:develop Dec 18, 2024
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@akesandgren akesandgren deleted the 20241213164029_new_pr_ABRicate100 branch December 19, 2024 07:20
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