{bio}[foss/2023a] metaWRAP v1.4-20230728 w/ Python 2.7.18

[PetrKralCZ]

resolves vscentrum/vsc-software-stack#494
needs

• {bio}[foss/2023a] QUAST v5.2.0 w/ Python 2.7.18 #22392
• {bio}[GCC/12.3.0,GCCcore/12.3.0,foss/2023a] CONCOCT v1.1.0, MEGAHIT v1.2.9, BEDTools v2.31.0 w/ Python 2.7.18 #22431

[github-actions]

Updated software metaWRAP-1.4-20230728-foss-2023a-Python-2.7.18.eb

Diff against metaWRAP-1.3-foss-2020b-Python-2.7.18.eb

easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.4-20230728-foss-2023a-Python-2.7.18.eb
index 382b15693e..771398962a 100644
--- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.4-20230728-foss-2023a-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'Tarball'
 
 name = 'metaWRAP'
-version = '1.3'
+version = '1.4-20230728'
+local_commit = 'c4a23f0'
 versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/bxlab/metaWRAP'
@@ -10,11 +11,11 @@ that accomplishes the core tasks of metagenomic analysis from start to finish:
 read quality control, assembly, visualization, taxonomic profiling, extracting
 draft genomes (binning), and functional annotation."""
 
-toolchain = {'name': 'foss', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = ['https://github.com/bxlab/metaWRAP/archive/']
-sources = ['v%(version)s.tar.gz']
-checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['f73cd1adb655e40b3bd40722414238bb2ea9dc62e6acef56abe3c8e44e8fe6f3']
 
 builddependencies = [
     ('Java', '11', '', SYSTEM),
@@ -23,30 +24,32 @@ builddependencies = [
 # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md
 dependencies = [
     ('Python', '2.7.18'),
-    ('Perl', '5.32.0'),
-    ('R', '4.0.3'),
-    ('BLAST+', '2.11.0'),
-    ('bmtagger', '3.101'),
-    ('Bowtie2', '2.4.2'),
-    ('BWA', '0.7.17'),
+    ('Perl', '5.36.1'),
+    ('R', '4.3.2'),
+    ('BLAST+', '2.14.1'),
+    ('bmtagger', '3.101', '-Java-11'),
+    ('Bowtie2', '2.5.4', versionsuffix),
+    ('BWA', '0.7.17'),  # 0.7.18?
     ('CheckM', '1.0.18', versionsuffix),
     ('FastQC', '0.11.9', '-Java-11', SYSTEM),
-    ('Kraken', '1.1.1'),
-    ('KronaTools', '2.8'),
+    ('Kraken2', '2.1.3'),  # previously Kraken
+    ('KronaTools', '2.8.1'),
     ('MEGAHIT', '1.2.9', versionsuffix),
-    ('MetaBAT', '2.15', versionsuffix),
+    ('MetaBAT', '2.17'),
     ('CONCOCT', '1.1.0', versionsuffix),
-    ('MaxBin', '2.2.7'),
-    ('QUAST', '5.0.2', versionsuffix),
-    ('SAMtools', '1.11'),
-    ('SPAdes', '3.15.2', versionsuffix),
-    ('Trim_Galore', '0.6.6', versionsuffix),
+    ('MaxBin', '2.2.7', versionsuffix),
+    ('QUAST', '5.2.0', versionsuffix),
+    ('SAMtools', '1.18'),  # 1.13?
+    ('SPAdes', '3.15.5', versionsuffix),
+    ('Trim_Galore', '0.6.10', versionsuffix),
     ('Seaborn', '0.9.1', versionsuffix),
-    ('Salmon', '1.4.0'),
-    ('taxator-tk', '1.3.3'),
+    ('Salmon', '1.10.3'),
+    ('taxator-tk', '1.5.0', versionsuffix),
     ('prokka', '1.14.5'),
 ]
 
+postinstallcmds = ['cd %(installdir)s/bin && ln -r -s metawrap metaWRAP']
+
 sanity_check_paths = {
     'files': ['bin/config-metawrap', 'bin/metaWRAP'],
     'dirs': [],

[PetrKralCZ]

@boegelbot please test @ jsc-zen3

[boegelbot]

@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=22432 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22432 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5847

Test results coming soon (I hope)...

Details

- notification for comment with ID 2695299065 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]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/f4dc0feffa2f0639ee0fbd948bf4b186 for a full test report.

[verdurin]

Test report by @verdurin
SUCCESS
Build succeeded for 13 out of 13 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10 (Green Obsidian), x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.8.17
See https://gist.github.com/verdurin/add048d83319eaa2558e12f5deaa2be6 for a full test report.

[verdurin]

Looks fine.

Request was addressed.

[verdurin]

Going in, thanks @PetrKralCZ!