{bio}[GCCcore/13.3.0] Gubbins v3.4.3, rapidNJ v2.3.3, SKA2 v0.3.7 #24642

verdurin · 2025-11-20T17:44:26Z

(created using eb --new-pr)

{devel}[GCCcore/13.3.0] Autoconf-archive v2024.10.16 #24664

…e-13.3.0.eb, SKA2-0.3.7-GCCcore-13.3.0.eb

github-actions · 2025-11-20T17:44:56Z

Updated software `Gubbins-3.4.3-foss-2024a.eb`

Diff against Gubbins-3.3.5-foss-2023a.eb

easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2023a.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.4.3-foss-2024a.eb
index 46e686e0f4..5281ee9e90 100644
--- a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.4.3-foss-2024a.eb
@@ -2,7 +2,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'Gubbins'
-version = '3.3.5'
+version = '3.4.3'
 
 homepage = "https://nickjcroucher.github.io/gubbins/"
 description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
@@ -11,34 +11,34 @@ description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide S
  Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term
  bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774']
+checksums = ['84489fa0ac83937ee22cd338c3633f74cb4fe6525b4700290a7f69e1eaec16e7']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('Autoconf-archive', '2023.02.20'),
-    ('pkgconf', '1.9.5'),
+    ('Autotools', '20231222'),
+    ('Autoconf-archive', '2024.10.16'),
+    ('pkgconf', '2.2.0'),
     ('Check', '0.15.2'),
-    ('subunit', '1.4.4'),
+    ('subunit', '1.4.5'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Biopython', '1.83'),
-    ('DendroPy', '4.6.1'),
-    ('numba', '0.58.1'),
-    ('SciPy-bundle', '2023.07'),
-    ('FastTree', '2.1.11'),
-    ('IQ-TREE', '2.3.5'),
+    ('Python', '3.12.3'),
+    ('Biopython', '1.84'),
+    ('DendroPy', '5.0.1'),
+    ('numba', '0.60.0'),
+    ('SciPy-bundle', '2024.05'),
+    ('FastTree', '2.2'),
+    ('IQ-TREE', '2.4.0'),
     ('rapidNJ', '2.3.3'),
     ('RAxML', '8.2.13'),
-    ('RAxML-NG', '1.2.0'),
+    ('RAxML-NG', '1.2.2'),
     ('SKA2', '0.3.7'),
-    ('dill', '0.3.7'),
-    ('multiprocess', '0.70.15'),
+    ('dill', '0.3.9'),
+    ('multiprocess', '0.70.17'),
 ]
 
 preconfigopts = "autoreconf -i && "

Diff against Gubbins-3.3.5-foss-2022b.eb

easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb

diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.4.3-foss-2024a.eb
index f7581cd7c2..5281ee9e90 100644
--- a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.4.3-foss-2024a.eb
@@ -2,7 +2,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'Gubbins'
-version = '3.3.5'
+version = '3.4.3'
 
 homepage = "https://nickjcroucher.github.io/gubbins/"
 description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
@@ -11,34 +11,34 @@ description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide S
  Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term
  bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774']
+checksums = ['84489fa0ac83937ee22cd338c3633f74cb4fe6525b4700290a7f69e1eaec16e7']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('Autoconf-archive', '2023.02.20'),
-    ('pkgconf', '1.9.3'),
+    ('Autotools', '20231222'),
+    ('Autoconf-archive', '2024.10.16'),
+    ('pkgconf', '2.2.0'),
     ('Check', '0.15.2'),
-    ('subunit', '1.4.3'),
+    ('subunit', '1.4.5'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('Biopython', '1.81'),
-    ('DendroPy', '4.5.2'),
-    ('numba', '0.58.1'),
-    ('SciPy-bundle', '2023.02'),
-    ('FastTree', '2.1.11'),
-    ('IQ-TREE', '2.2.2.6'),
+    ('Python', '3.12.3'),
+    ('Biopython', '1.84'),
+    ('DendroPy', '5.0.1'),
+    ('numba', '0.60.0'),
+    ('SciPy-bundle', '2024.05'),
+    ('FastTree', '2.2'),
+    ('IQ-TREE', '2.4.0'),
     ('rapidNJ', '2.3.3'),
-    ('RAxML', '8.2.12', '-avx2'),
-    ('RAxML-NG', '1.2.0'),
+    ('RAxML', '8.2.13'),
+    ('RAxML-NG', '1.2.2'),
     ('SKA2', '0.3.7'),
-    ('dill', '0.3.7'),
-    ('multiprocess', '0.70.15'),
+    ('dill', '0.3.9'),
+    ('multiprocess', '0.70.17'),
 ]
 
 preconfigopts = "autoreconf -i && "

Updated software `rapidNJ-2.3.3-GCCcore-13.3.0.eb`

Diff against rapidNJ-2.3.3-GCCcore-12.3.0.eb

easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
index 1db19edeef..5e74cb2c1f 100644
--- a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
@@ -20,13 +20,13 @@ In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI
 Springer Verlag, October 2008.
 doi: 10.1007/978-3-540-87361-7_10"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/somme89/rapidNJ/archive/']
 sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}]
 checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
 files_to_copy = [(['bin/rapidnj'], 'bin')]

Diff against rapidNJ-2.3.3-GCCcore-12.2.0.eb

easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
index cb927fd4c4..5e74cb2c1f 100644
--- a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
@@ -20,13 +20,13 @@ In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI
 Springer Verlag, October 2008.
 doi: 10.1007/978-3-540-87361-7_10"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/somme89/rapidNJ/archive/']
 sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}]
 checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d']
 
-builddependencies = [('binutils', '2.39')]
+builddependencies = [('binutils', '2.42')]
 
 files_to_copy = [(['bin/rapidnj'], 'bin')]

Diff against rapidNJ-2.3.3-GCCcore-11.3.0.eb

easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
index 07fb5750f5..5e74cb2c1f 100644
--- a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-13.3.0.eb
@@ -20,13 +20,13 @@ In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI
 Springer Verlag, October 2008.
 doi: 10.1007/978-3-540-87361-7_10"""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/somme89/rapidNJ/archive/']
 sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}]
 checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d']
 
-builddependencies = [('binutils', '2.38')]
+builddependencies = [('binutils', '2.42')]
 
 files_to_copy = [(['bin/rapidnj'], 'bin')]

Updated software `SKA2-0.3.7-GCCcore-13.3.0.eb`

Diff against SKA2-0.3.7-GCCcore-12.3.0.eb

easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-13.3.0.eb
index a0950a90e0..8058435a61 100644
--- a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-13.3.0.eb
@@ -7,7 +7,7 @@ homepage = 'https://docs.rs/ska/latest/ska/'
 description = """Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely
  related sequences, typically small haploid genomes such as bacteria and viruses."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = []
 checksums = [
@@ -381,8 +381,8 @@ crates = [
 ]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('Rust', '1.75.0'),
+    ('binutils', '2.42'),
+    ('Rust', '1.79.0'),
 ]
 
 sanity_check_paths = {

Diff against SKA2-0.3.7-GCCcore-12.2.0.eb

easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-13.3.0.eb
index ec330ffc75..8058435a61 100644
--- a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-13.3.0.eb
@@ -7,7 +7,7 @@ homepage = 'https://docs.rs/ska/latest/ska/'
 description = """Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely
  related sequences, typically small haploid genomes such as bacteria and viruses."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = []
 checksums = [
@@ -381,8 +381,8 @@ crates = [
 ]
 
 builddependencies = [
-    ('binutils', '2.39'),
-    ('Rust', '1.75.0'),
+    ('binutils', '2.42'),
+    ('Rust', '1.79.0'),
 ]
 
 sanity_check_paths = {

…asyconfigs into 20251120174423_new_pr_Gubbins343

verdurin · 2025-11-25T15:47:17Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (3 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 3.11.13
See https://gist.github.com/verdurin/a91ac2239c2428d4424d18bd6c01c30b for a full test report.

verdurin · 2025-11-25T15:47:59Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-11-25T15:50:10Z

@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=24642 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24642 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8902

Test results coming soon (I hope)...

- notification for comment with ID 3576326613 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 · 2025-11-25T15:57:57Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (total: 5 mins 42 secs) (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/35c1f199664686e223df9be0ff82e432 for a full test report.

adding easyconfigs: Gubbins-3.4.3-foss-2024a.eb, rapidNJ-2.3.3-GCCcor…

da82de8

…e-13.3.0.eb, SKA2-0.3.7-GCCcore-13.3.0.eb

verdurin added the update label Nov 20, 2025

github-actions bot added the 2024a issues & PRs related to 2024a common toolchains label Nov 20, 2025

Micket and others added 3 commits November 21, 2025 16:11

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

e35b6dc

…asyconfigs into 20251120174423_new_pr_Gubbins343

Fix python invocation

f670e0d

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

15c3297

…asyconfigs into 20251120174423_new_pr_Gubbins343

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{bio}[GCCcore/13.3.0] Gubbins v3.4.3, rapidNJ v2.3.3, SKA2 v0.3.7 #24642

{bio}[GCCcore/13.3.0] Gubbins v3.4.3, rapidNJ v2.3.3, SKA2 v0.3.7 #24642

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{bio}[GCCcore/13.3.0] Gubbins v3.4.3, rapidNJ v2.3.3, SKA2 v0.3.7 #24642

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Updated software Gubbins-3.4.3-foss-2024a.eb

Updated software rapidNJ-2.3.3-GCCcore-13.3.0.eb

Updated software SKA2-0.3.7-GCCcore-13.3.0.eb

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Updated software `Gubbins-3.4.3-foss-2024a.eb`

Updated software `rapidNJ-2.3.3-GCCcore-13.3.0.eb`

Updated software `SKA2-0.3.7-GCCcore-13.3.0.eb`