{bio}[foss/2023a] Tombo v1.5.1

[verdurin]

(created using eb --new-pr)

[github-actions]

Updated software Tombo-1.5.1-foss-2023a.eb

Diff against Tombo-1.5.1-foss-2019b-Python-3.7.4.eb

easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb

diff --git a/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb
index c5910bd996..b4191a47cf 100644
--- a/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb
@@ -5,20 +5,19 @@ easyblock = 'PythonBundle'
 
 name = 'Tombo'
 version = '1.5.1'
-versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/nanoporetech/tombo'
 description = """Tombo is a suite of tools primarily for the identification of modified nucleotides
  from raw nanopore sequencing data."""
 
-toolchain = {'name': 'foss', 'version': '2019b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.7.4'),
-    ('SciPy-bundle', '2019.10', versionsuffix),
-    ('h5py', '2.10.0', versionsuffix),
-    ('tqdm', '4.41.1'),
-    ('rpy2', '3.2.6', versionsuffix),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+    ('tqdm', '4.66.1'),
+    ('rpy2', '3.5.15'),
 ]
 
 use_pip = True
@@ -27,16 +26,16 @@ exts_list = [
     ('pyfaidx', '0.5.8', {
         'checksums': ['58f0ff57a875af7e69a12cf1e7086efa4976919ac4dcebbc5f3def6fd4881d0d'],
     }),
-    ('mappy', '2.17', {
-        'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'],
+    ('mappy', '2.28', {
+        'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
     }),
     ('ont-tombo', version, {
         'modulename': 'tombo',
         'patches': ['Tombo-%(version)s_rpy2-v3.patch'],
         'use_pip_extras': 'full',
         'checksums': [
-            'f5ae8f4c5fc1ab212306ff14ae93fbd1c1034421148ff2e728f169f69a824380',  # ont-tombo-1.5.1.tar.gz
-            '0d9e5e96aa741b70acbbddbf0d403f55878bdb956def57f1332a4b0d7582a8ff',  # Tombo-1.5.1_rpy2-v3.patch
+            {'ont-tombo-1.5.1.tar.gz': 'f5ae8f4c5fc1ab212306ff14ae93fbd1c1034421148ff2e728f169f69a824380'},
+            {'Tombo-1.5.1_rpy2-v3.patch': '0d9e5e96aa741b70acbbddbf0d403f55878bdb956def57f1332a4b0d7582a8ff'},
         ],
     }),
 ]

[verdurin]

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 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/4417df3646322f7d5460a14d516cd79d for a full test report.

[verdurin]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=21925 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21925 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14778

Test results coming soon (I hope)...

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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)
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/5abfbbff7639adffc14deb22ea783a5f for a full test report.

[verdurin]

@boegelbot please test @ jsc-zen3

[boegelbot]

@verdurin: 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=21925 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21925 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5350

Test results coming soon (I hope)...

- notification for comment with ID 2506540840 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 3.9.19
See https://gist.github.com/boegelbot/e96cbef05145a674460148559423f5da for a full test report.