Skip to content

{bio}[foss/2023a] metaWRAP v1.4-20230728 w/ Python 2.7.18#22432

Merged
verdurin merged 5 commits intoeasybuilders:developfrom
PetrKralCZ:20250303112321_new_pr_metaWRAP1420230728
Mar 26, 2025
Merged

{bio}[foss/2023a] metaWRAP v1.4-20230728 w/ Python 2.7.18#22432
verdurin merged 5 commits intoeasybuilders:developfrom
PetrKralCZ:20250303112321_new_pr_metaWRAP1420230728

Conversation

@github-actions github-actions bot added the update label Mar 3, 2025
@github-actions
Copy link

github-actions bot commented Mar 3, 2025

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 PetrKralCZ marked this pull request as ready for review March 3, 2025 11:32
PetrKralCZ and others added 2 commits March 3, 2025 17:34
…23a-Python-2.7.18.eb

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>
@PetrKralCZ
Copy link
Collaborator Author

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

@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
Copy link
Collaborator

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
Copy link
Member

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.

Copy link
Member

@verdurin verdurin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks fine.

@verdurin verdurin dismissed branfosj’s stale review March 26, 2025 12:20

Request was addressed.

@verdurin verdurin added this to the release after 5.0.0 milestone Mar 26, 2025
@verdurin
Copy link
Member

Going in, thanks @PetrKralCZ!

@verdurin verdurin merged commit 1159c8b into easybuilders:develop Mar 26, 2025
8 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

Projects

None yet

Development

Successfully merging this pull request may close these issues.

MetaWRAP

4 participants