{bio}[GCCcore/14.2.0] Infernal v1.1.5, ARAGORN v1.2.41, MinCED v0.4.2, ... by JarneRenders · Pull Request #25037 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-01-12T15:58:56Z

(created using eb --new-pr)

…core-14.2.0.eb, MinCED-0.4.2-GCCcore-14.2.0.eb, prodigal-2.6.3-GCCcore-14.2.0.eb

github-actions · 2026-01-12T15:59:27Z

Updated software `ARAGORN-1.2.41-GCC-14.2.0.eb`

Diff against ARAGORN-1.2.41-foss-2021b.eb

easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb

diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-GCC-14.2.0.eb
index f596bc6846..34659d42ff 100644
--- a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-GCC-14.2.0.eb
@@ -9,12 +9,12 @@ easyblock = 'CmdCp'
 name = 'ARAGORN'
 version = '1.2.41'
 
-homepage = 'http://www.ansikte.se/ARAGORN/'
+homepage = 'https://www.trna.se/ARAGORN/'
 description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences"
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'GCC', 'version': '14.2.0'}
 
-source_urls = ['http://www.ansikte.se/ARAGORN/Downloads/']
+source_urls = ['https://www.trna.se/ARAGORN/Downloads/']
 sources = [
     {'filename': '%(namelower)s%(version)s.c', 'extract_cmd': 'cp %s aragorn.c'},
     {'download_filename': 'aragorn.1', 'filename': 'aragorn-%(version)s.man', 'extract_cmd': 'cp %s aragorn.1'}

Updated software `Infernal-1.1.5-gompi-2025a.eb`

Diff against Infernal-1.1.5-gompi-2023a.eb

easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2023a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
index b6549b1fd9..3672dd1ac2 100644
--- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2023a.eb
+++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
@@ -20,7 +20,7 @@ homepage = 'http://eddylab.org/infernal/'
 description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
  for RNA structure and sequence similarities."""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['http://eddylab.org/%(namelower)s']

Diff against Infernal-1.1.4-gompi-2022b.eb

easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
index d8241c2a80..3672dd1ac2 100644
--- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022b.eb
+++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
@@ -14,18 +14,18 @@
 easyblock = 'ConfigureMake'
 
 name = 'Infernal'
-version = "1.1.4"
+version = "1.1.5"
 
 homepage = 'http://eddylab.org/infernal/'
 description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
  for RNA structure and sequence similarities."""
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['http://eddylab.org/%(namelower)s']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc']
+checksums = ['ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f']
 
 # MPI is disabled by default
 configopts = '--enable-mpi'

Diff against Infernal-1.1.4-gompi-2022a.eb

easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
index be7cd33cd2..3672dd1ac2 100644
--- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2022a.eb
+++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-gompi-2025a.eb
@@ -14,18 +14,18 @@
 easyblock = 'ConfigureMake'
 
 name = 'Infernal'
-version = "1.1.4"
+version = "1.1.5"
 
 homepage = 'http://eddylab.org/infernal/'
 description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
  for RNA structure and sequence similarities."""
 
-toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchain = {'name': 'gompi', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['http://eddylab.org/%(namelower)s']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc']
+checksums = ['ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f']
 
 # MPI is disabled by default
 configopts = '--enable-mpi'

Updated software `prodigal-2.6.3-GCCcore-14.2.0.eb`

Diff against prodigal-2.6.3-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
index 74f0d81718..d70afd7b43 100644
--- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
@@ -22,7 +22,7 @@ description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm
    is a microbial (bacterial and archaeal) gene finding program developed
    at Oak Ridge National Laboratory and the University of Tennessee."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
 sources = ['v%(version)s.tar.gz']

Diff against prodigal-2.6.3-GCCcore-13.2.0.eb

easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
index 22a2163f6d..d70afd7b43 100644
--- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
@@ -22,13 +22,13 @@ description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm
    is a microbial (bacterial and archaeal) gene finding program developed
    at Oak Ridge National Laboratory and the University of Tennessee."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
 files_to_copy = [
     (['prodigal'], 'bin'),

Diff against prodigal-2.6.3-GCCcore-12.3.0.eb

easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
index 09e71ae376..d70afd7b43 100644
--- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-14.2.0.eb
@@ -22,13 +22,13 @@ description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm
    is a microbial (bacterial and archaeal) gene finding program developed
    at Oak Ridge National Laboratory and the University of Tennessee."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
 files_to_copy = [
     (['prodigal'], 'bin'),

jfgrimm · 2026-01-13T16:34:10Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 4 out of 4 (total: 3 mins 53 secs) (4 easyconfigs in total)
node031.viking2.yor.alces.network - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/19a4eda479d8329c64913c2e21743ebb for a full test report.

jfgrimm · 2026-01-13T16:34:53Z

@boegelbot: please test @ jsc-zen3

boegelbot · 2026-01-13T16:40:09Z

@jfgrimm: 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=25037 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25037 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9386

Test results coming soon (I hope)...

Details

- notification for comment with ID 3745296520 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 · 2026-01-13T16:44:37Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 4 mins 11 secs) (4 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/02717bc20aefd40858303e6d6f4ed2f3 for a full test report.

jfgrimm

lgtm

jfgrimm · 2026-01-13T16:55:25Z

Going in, thanks @JarneRenders!

adding easyconfigs: Infernal-1.1.5-gompi-2025a.eb, ARAGORN-1.2.41-GCC…

3a5fdb0

…core-14.2.0.eb, MinCED-0.4.2-GCCcore-14.2.0.eb, prodigal-2.6.3-GCCcore-14.2.0.eb

github-actions Bot added 2025a issues & PRs related to 2025a common toolchains new update labels Jan 12, 2026

JarneRenders mentioned this pull request Jan 12, 2026

{bio}[GCCcore/14.2.0,gompi/2025a] table2asn v20250916, prokka v1.15.6 #25039

Merged

2 tasks

Add GCC and binutils deps

407c784

jfgrimm added this to the next release (5.2.1?) milestone Jan 13, 2026

jfgrimm approved these changes Jan 13, 2026

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jfgrimm merged commit 0ae9a2e into easybuilders:develop Jan 13, 2026
8 checks passed

JarneRenders deleted the 20260112165848_new_pr_Infernal115 branch January 14, 2026 10:23

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{bio}[GCCcore/14.2.0] Infernal v1.1.5, ARAGORN v1.2.41, MinCED v0.4.2, ...#25037

{bio}[GCCcore/14.2.0] Infernal v1.1.5, ARAGORN v1.2.41, MinCED v0.4.2, ...#25037
jfgrimm merged 2 commits intoeasybuilders:developfrom
JarneRenders:20260112165848_new_pr_Infernal115

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Updated software ARAGORN-1.2.41-GCC-14.2.0.eb

Updated software Infernal-1.1.5-gompi-2025a.eb

Updated software prodigal-2.6.3-GCCcore-14.2.0.eb

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github-actions Bot commented Jan 12, 2026 •

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Updated software `ARAGORN-1.2.41-GCC-14.2.0.eb`

Updated software `Infernal-1.1.5-gompi-2025a.eb`

Updated software `prodigal-2.6.3-GCCcore-14.2.0.eb`