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{2026.06}[GCC/15.2.0,GCCcore/15.2.0] BEDTools 2.31.1, SAMtools 1.23.1, GATK 4.6.2.0 - #1773

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HaoZeke wants to merge 4 commits into
EESSI:mainfrom
HaoZeke:2026.06-genomics
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{2026.06}[GCC/15.2.0,GCCcore/15.2.0] BEDTools 2.31.1, SAMtools 1.23.1, GATK 4.6.2.0#1773
HaoZeke wants to merge 4 commits into
EESSI:mainfrom
HaoZeke:2026.06-genomics

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@HaoZeke

@HaoZeke HaoZeke commented Oct 11, 2026

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Adds BEDTools-2.31.1-GCC-15.2.0, SAMtools-1.23.1-GCC-15.2.0, GATK-4.6.2.0-GCCcore-15.2.0-Java-25 to 2026.06. Recipes after the EasyBuild 5.4.0 release are pinned with from-commit to their merge commit on develop.

@HaoZeke

HaoZeke commented Oct 11, 2026

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bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen4
bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=aarch64/generic

@eessi-bot-aws

eessi-bot-aws Bot commented Oct 11, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-software
Building on: amd-zen4
Building for: x86_64/amd/zen4
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_1773/206282

date job status comment
Oct 11 18:35:49 UTC 2026 submitted job id 206282 awaits release by job manager
Oct 11 18:36:30 UTC 2026 released job awaits launch by Slurm scheduler
Oct 11 18:45:23 UTC 2026 running job 206282 is running
Oct 11 18:53:41 UTC 2026 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-206282.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2026.06-software-linux-x86_64-amd-zen4-17917446580.tar.zstsize: 827 MiB (868051271 bytes)
entries: 2250
modules under 2026.06/software/linux/x86_64/amd/zen4/modules/all
BEDTools/2.31.1-GCC-15.2.0.lua
GATK/4.6.2.0-GCCcore-15.2.0-Java-25.lua
Java/25.36.lua
Java/.modulerc.lua
SAMtools/1.23.1-GCC-15.2.0.lua
software under 2026.06/software/linux/x86_64/amd/zen4/software
BEDTools/2.31.1-GCC-15.2.0
GATK/4.6.2.0-GCCcore-15.2.0-Java-25
Java/25.36
SAMtools/1.23.1-GCC-15.2.0
reprod directories under 2026.06/software/linux/x86_64/amd/zen4/reprod
BEDTools/2.31.1-GCC-15.2.0/20261011_184630UTC
GATK/4.6.2.0-GCCcore-15.2.0-Java-25/20261011_184836UTC
Java/25.36/20261011_184822UTC
SAMtools/1.23.1-GCC-15.2.0/20261011_184727UTC
other under 2026.06/software/linux/x86_64/amd/zen4
no other files in tarball
Oct 11 18:53:41 UTC 2026 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 0/0 test case(s) from 0 check(s) (0 failure(s), 0 expected failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-206282.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Oct 11, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-software
Building on: generic
Building for: aarch64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_1773/206283

date job status comment
Oct 11 18:35:55 UTC 2026 submitted job id 206283 awaits release by job manager
Oct 11 18:36:21 UTC 2026 released job awaits launch by Slurm scheduler
Oct 11 18:41:56 UTC 2026 running job 206283 is running
Oct 11 18:51:17 UTC 2026 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-206283.out
✅ no message matching FATAL:
✅ no message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2026.06-software-linux-aarch64-generic-17917445660.tar.zstsize: 826 MiB (866413237 bytes)
entries: 2249
modules under 2026.06/software/linux/aarch64/generic/modules/all
BEDTools/2.31.1-GCC-15.2.0.lua
GATK/4.6.2.0-GCCcore-15.2.0-Java-25.lua
Java/25.36.lua
Java/.modulerc.lua
SAMtools/1.23.1-GCC-15.2.0.lua
software under 2026.06/software/linux/aarch64/generic/software
BEDTools/2.31.1-GCC-15.2.0
GATK/4.6.2.0-GCCcore-15.2.0-Java-25
Java/25.36
SAMtools/1.23.1-GCC-15.2.0
reprod directories under 2026.06/software/linux/aarch64/generic/reprod
BEDTools/2.31.1-GCC-15.2.0/20261011_184409UTC
GATK/4.6.2.0-GCCcore-15.2.0-Java-25/20261011_184603UTC
Java/25.36/20261011_184546UTC
SAMtools/1.23.1-GCC-15.2.0/20261011_184456UTC
other under 2026.06/software/linux/aarch64/generic
no other files in tarball
Oct 11 18:51:17 UTC 2026 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 0/0 test case(s) from 0 check(s) (0 failure(s), 0 expected failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-206283.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

casparvl
casparvl reviewed Oct 21, 2026
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Comment thread easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml Outdated
Comment on lines +154 to +159
- BEDTools-2.31.1-GCC-15.2.0.eb:
options:
# see https://github.com/easybuilders/easybuild-easyconfigs/pull/26634
from-commit: 097f4708abcfd5b29a607013475f71de708efc8e
- SAMtools-1.23.1-GCC-15.2.0.eb
- GATK-4.6.2.0-GCCcore-15.2.0-Java-25.eb

@casparvl casparvl Oct 21, 2026

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EasyBuild 5.4.1 is out, which contains this BEDTools as well. Mind bumping these to a new 5.4.1-based easystack, so we don't need to use the from-commit?

@HaoZeke
move BEDTools, SAMtools and GATK to EB 5.4.1 easystack
cdf203a 
EasyBuild 5.4.1 ships BEDTools 2.31.1, SAMtools 1.23.1 and GATK 4.6.2.0,
so the from-commit pin is no longer needed.
@casparvl

casparvl commented Oct 22, 2026

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bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2
bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=aarch64/generic

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@casparvl

casparvl commented Oct 22, 2026

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bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2
bot: build repo:eessi.io-2026.06-software instance:eessi-bot-mc-aws for:arch=aarch64/generic

@eessi-bot-aws

eessi-bot-aws Bot commented Oct 22, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_1773/212683

date job status comment
Oct 22 09:12:37 UTC 2026 submitted job id 212683 awaits release by job manager
Oct 22 09:13:02 UTC 2026 released job awaits launch by Slurm scheduler
Oct 22 09:23:13 UTC 2026 running job 212683 is running
Oct 22 09:30:33 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-212683.out
✅ no message matching FATAL:
❌ found message matching ERROR:
✅ no message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2026.06-software-linux-x86_64-amd-zen2-17926613350.tar.zstsize: 827 MiB (868020132 bytes)
entries: 2250
modules under 2026.06/software/linux/x86_64/amd/zen2/modules/all
BEDTools/2.31.1-GCC-15.2.0.lua
GATK/4.6.2.0-GCCcore-15.2.0-Java-25.lua
Java/25.36.lua
Java/.modulerc.lua
SAMtools/1.23.1-GCC-15.2.0.lua
software under 2026.06/software/linux/x86_64/amd/zen2/software
BEDTools/2.31.1-GCC-15.2.0
GATK/4.6.2.0-GCCcore-15.2.0-Java-25
Java/25.36
SAMtools/1.23.1-GCC-15.2.0
reprod directories under 2026.06/software/linux/x86_64/amd/zen2/reprod
BEDTools/2.31.1-GCC-15.2.0/20261022_092502UTC
GATK/4.6.2.0-GCCcore-15.2.0-Java-25/20261022_092839UTC
Java/25.36/20261022_092817UTC
SAMtools/1.23.1-GCC-15.2.0/20261022_092636UTC
other under 2026.06/software/linux/x86_64/amd/zen2
no other files in tarball
Oct 22 09:30:33 UTC 2026 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 0/0 test case(s) from 0 check(s) (0 failure(s), 0 expected failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-212683.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Oct 22, 2026 •
edited
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New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-software
Building on: generic
Building for: aarch64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_1773/212684

date job status comment
Oct 22 09:12:43 UTC 2026 submitted job id 212684 awaits release by job manager
Oct 22 09:12:59 UTC 2026 released job awaits launch by Slurm scheduler
Oct 22 09:20:05 UTC 2026 running job 212684 is running
Oct 22 09:28:28 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-212684.out
✅ no message matching FATAL:
❌ found message matching ERROR:
✅ no message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2026.06-software-linux-aarch64-generic-17926612140.tar.zstsize: 826 MiB (866469890 bytes)
entries: 2249
modules under 2026.06/software/linux/aarch64/generic/modules/all
BEDTools/2.31.1-GCC-15.2.0.lua
GATK/4.6.2.0-GCCcore-15.2.0-Java-25.lua
Java/25.36.lua
Java/.modulerc.lua
SAMtools/1.23.1-GCC-15.2.0.lua
software under 2026.06/software/linux/aarch64/generic/software
BEDTools/2.31.1-GCC-15.2.0
GATK/4.6.2.0-GCCcore-15.2.0-Java-25
Java/25.36
SAMtools/1.23.1-GCC-15.2.0
reprod directories under 2026.06/software/linux/aarch64/generic/reprod
BEDTools/2.31.1-GCC-15.2.0/20261022_092414UTC
GATK/4.6.2.0-GCCcore-15.2.0-Java-25/20261022_092638UTC
Java/25.36/20261022_092618UTC
SAMtools/1.23.1-GCC-15.2.0/20261022_092525UTC
other under 2026.06/software/linux/aarch64/generic
no other files in tarball
Oct 22 09:28:28 UTC 2026 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 0/0 test case(s) from 0 check(s) (0 failure(s), 0 expected failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-212684.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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3 participants

@HaoZeke @casparvl @trz42