{bio}[GCCcore/14.3.0] cutadapt v5.1 by sxpl-DavidSchmidt · Pull Request #24835 · easybuilders/easybuild-easyconfigs

sxpl-DavidSchmidt · 2025-12-11T14:49:23Z

(created using eb --new-pr)
depends on PRs:

{lib}[GCCcore/14.3.0] python-isal v1.8.0 #24872

github-actions · 2025-12-11T14:49:53Z

Updated software `cutadapt-5.1-GCCcore-14.3.0.eb`

Diff against cutadapt-5.1-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
index e79a65e718..c5b1abbb33 100644
--- a/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
@@ -18,26 +18,27 @@ homepage = 'https://opensource.scilifelab.se/projects/cutadapt/'
 description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and
  other types of unwanted sequence from your high-throughput sequencing reads."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('Cython', '3.0.10'),  # required for dnaio
+    ('binutils', '2.44'),
+    ('Cython', '3.1.2'),  # required for dnaio
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.13.5'),
     ('pigz', '2.8'),
-    ('python-isal', '1.7.0'),
-    ('zlib-ng', '2.2.1'),
+    ('python-isal', '1.8.0'),
+    ('zlib-ng', '2.2.5'),
+    ('python-zlib-ng', '0.5.1'),
 ]
 
 exts_list = [
     ('xopen', '2.0.2', {
         'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154'],
     }),
-    ('dnaio', '1.2.3', {
-        'checksums': ['aad456d9f6272339958b2c5af32fd64d77a50aca12e394e7a143b4129d49b0b9'],
+    ('dnaio', '1.2.4', {
+        'checksums': ['a7570311f29e8b3c1ea39a60f57b7baf8dad8f2508595c58d4278c5571463166'],
     }),
     (name, version, {
         'patches': ['cutadapt-%(version)s_old_setuptools.patch'],

Diff against cutadapt-5.0-GCCcore-13.2.0.eb

easybuild/easyconfigs/c/cutadapt/cutadapt-5.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
index 067bb56066..c5b1abbb33 100644
--- a/easybuild/easyconfigs/c/cutadapt/cutadapt-5.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
@@ -12,34 +12,40 @@
 easyblock = 'PythonBundle'
 
 name = 'cutadapt'
-version = '5.0'
+version = '5.1'
 
 homepage = 'https://opensource.scilifelab.se/projects/cutadapt/'
 description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and
  other types of unwanted sequence from your high-throughput sequencing reads."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('Cython', '3.0.10'),  # required for dnaio
+    ('binutils', '2.44'),
+    ('Cython', '3.1.2'),  # required for dnaio
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
+    ('Python', '3.13.5'),
     ('pigz', '2.8'),
-    ('python-isal', '1.6.1'),
+    ('python-isal', '1.8.0'),
+    ('zlib-ng', '2.2.5'),
+    ('python-zlib-ng', '0.5.1'),
 ]
 
 exts_list = [
-    ('xopen', '1.7.0', {
-        'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'],
+    ('xopen', '2.0.2', {
+        'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154'],
     }),
-    ('dnaio', '1.2.3', {
-        'checksums': ['aad456d9f6272339958b2c5af32fd64d77a50aca12e394e7a143b4129d49b0b9'],
+    ('dnaio', '1.2.4', {
+        'checksums': ['a7570311f29e8b3c1ea39a60f57b7baf8dad8f2508595c58d4278c5571463166'],
     }),
     (name, version, {
-        'checksums': ['cd66872b6635c068cf223f72fb0cc93b2454088a3e807a550bb36f717d25ae29'],
+        'patches': ['cutadapt-%(version)s_old_setuptools.patch'],
+        'checksums': [
+            {'cutadapt-5.1.tar.gz': '6bc76345c0a45f6b680cb1164e48eb1f81815c764ec471284ab6234c6653b937'},
+            {'cutadapt-5.1_old_setuptools.patch': '2185557c761d1b53676f0ca16725dbef08c5e50cd57967f88db3dee84ee2ea44'},
+        ],
     }),
 ]

Diff against cutadapt-1.18-GCCcore-12.3.0-Python-2.7.18.eb

easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-12.3.0-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
index ff4ac2a515..c5b1abbb33 100644
--- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-12.3.0-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb
@@ -4,39 +4,48 @@
 # Biozentrum - University of Basel
 # Modified by: Adam Huffman, Jonas Demeulemeester
 # The Francis Crick Institute
-# Modufied by: Albert Bogdanowicz
+# Modified by: Albert Bogdanowicz
 # Institute of Biochemistry and Biophysics PAS
-# Update: Petr Král (INUITS)
+# Modified by: Jasper Grimm
+# University of York
 
 easyblock = 'PythonBundle'
 
 name = 'cutadapt'
-version = '1.18'
-versionsuffix = '-Python-%(pyver)s'
+version = '5.1'
 
 homepage = 'https://opensource.scilifelab.se/projects/cutadapt/'
-description = """Cutadapt finds and removes adapter sequences, primers, poly-A
-tails and other types of unwanted sequence from your high-throughput sequencing
-reads."""
+description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and
+ other types of unwanted sequence from your high-throughput sequencing reads."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('NASM', '2.16.01'),
+    ('binutils', '2.44'),
+    ('Cython', '3.1.2'),  # required for dnaio
 ]
 
-dependencies = [('Python', '2.7.18')]
+dependencies = [
+    ('Python', '3.13.5'),
+    ('pigz', '2.8'),
+    ('python-isal', '1.8.0'),
+    ('zlib-ng', '2.2.5'),
+    ('python-zlib-ng', '0.5.1'),
+]
 
 exts_list = [
-    ('bz2file', '0.98', {
-        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    ('xopen', '2.0.2', {
+        'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154'],
     }),
-    ('xopen', '0.8.4', {
-        'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'],
+    ('dnaio', '1.2.4', {
+        'checksums': ['a7570311f29e8b3c1ea39a60f57b7baf8dad8f2508595c58d4278c5571463166'],
     }),
     (name, version, {
-        'checksums': ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'],
+        'patches': ['cutadapt-%(version)s_old_setuptools.patch'],
+        'checksums': [
+            {'cutadapt-5.1.tar.gz': '6bc76345c0a45f6b680cb1164e48eb1f81815c764ec471284ab6234c6653b937'},
+            {'cutadapt-5.1_old_setuptools.patch': '2185557c761d1b53676f0ca16725dbef08c5e50cd57967f88db3dee84ee2ea44'},
+        ],
     }),
 ]
 
@@ -47,7 +56,7 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     "cutadapt --help",
-    "python -c 'import cutadapt.seqio'",  # requires xopen
+    "cutadapt --version",
 ]
 
 moduleclass = 'bio'

…asyconfigs into 20251211154916_new_pr_cutadapt51

boegel · 2026-04-08T08:32:59Z

easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb

+]
+
+exts_list = [
+    ('zlib-ng', '1.0.0', {


We should use the existing python-zlib-ng as a dependency instead, I'll add a commit to make that change so we can get this merged...

…e as extension in easyconfig for cutadapt 5.1

boegel · 2026-04-08T08:39:51Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-04-08T08:50:14Z

@boegel: 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=24835 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24835 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10150

Test results coming soon (I hope)...

Details

- notification for comment with ID 4204949034 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 · 2026-04-08T08:53:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 2 mins 54 secs) (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/b4e596026866dbb41eb940e230687eec for a full test report.

boegel · 2026-04-08T09:00:40Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (total: 42 secs) (1 easyconfigs in total)
node4401.skiddo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9755 128-Core Processor (zen5), Python 3.9.21
See https://gist.github.com/boegel/b27053ec49c10b6deaf15d49454ba3fc for a full test report.

boegel · 2026-04-08T09:16:29Z

easybuild/easyconfigs/c/cutadapt/cutadapt-5.1-GCCcore-14.3.0.eb

+easyblock = 'PythonBundle'
+
+name = 'cutadapt'
+version = '5.1'


@sxpl-DavidSchmidt Any reason you didn't update this to 5.2, which has been available since Oct'25?

adding easyconfigs: cutadapt-5.1-GCCcore-14.3.0.eb

74a39aa

github-actions bot added 2025b issues & PRs related to 2025b common toolchains update labels Dec 11, 2025

Update cutadapt-5.1-GCCcore-14.3.0.eb

4c56ed6

sxpl-DavidSchmidt mentioned this pull request Dec 15, 2025

{tools}[GCCcore/14.3.0] zlib-ng v2.3.2 #24834

Closed

Fixed mixed indentation

5aba525

Thyre mentioned this pull request Feb 10, 2026

{lib}[GCCcore/14.3.0] python-isal v1.8.0 #24833

Closed

boegel added this to the next release (5.3.0) milestone Apr 8, 2026

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

b5dcafc

…asyconfigs into 20251211154916_new_pr_cutadapt51

boegel reviewed Apr 8, 2026

View reviewed changes

python-zlib-ng dependency instead of installing zlib-ng Python packag…

c01dcdb

…e as extension in easyconfig for cutadapt 5.1

boegel requested changes Apr 8, 2026

View reviewed changes

boegel modified the milestones: next release (5.3.0), 5.x Apr 8, 2026

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{bio}[GCCcore/14.3.0] cutadapt v5.1#24835

{bio}[GCCcore/14.3.0] cutadapt v5.1#24835
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sxpl-DavidSchmidt:20251211154916_new_pr_cutadapt51

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Updated software cutadapt-5.1-GCCcore-14.3.0.eb

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sxpl-DavidSchmidt commented Dec 11, 2025 •

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Updated software `cutadapt-5.1-GCCcore-14.3.0.eb`