stick to QIIME2 2024.2.0 with foss/2023a, since recent versions (like 2024.10.0) require a more recent version of `pandas` by pavelToman · Pull Request #22904 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-05-16T09:54:01Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#521

incompatibility with older pandas version emerges via error message like:

Plugin error from dada2:

  'DataFrame' object has no attribute 'map'

…licon.eb

pavelToman · 2025-05-16T10:03:45Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-16T10:10:08Z

@pavelToman: 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=22904 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22904 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6362

Test results coming soon (I hope)...

Details

- notification for comment with ID 2886267101 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 · 2025-05-16T10:31:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/f6b68ed17bb39cab824f9a13a75720cc for a full test report.

pavelToman · 2025-05-16T14:45:37Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3309.joltik.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, Python 3.9.18
See https://gist.github.com/pavelToman/dcbe9c89ae83fd3ad9672c7097fd8495 for a full test report.

pavelToman · 2025-05-16T14:45:38Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4016.donphan.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 570.86.15, Python 3.9.18
See https://gist.github.com/pavelToman/f6f384f0f6215154d84a21049b367173 for a full test report.

pavelToman · 2025-05-19T13:35:27Z

Test report by @pavelToman
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node4242.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/283d8a57c2c46e960c739ca1412a59a7 for a full test report.

pavelToman · 2025-05-20T11:20:34Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-20T11:30:10Z

@pavelToman: 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=22904 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22904 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6398

Test results coming soon (I hope)...

Details

- notification for comment with ID 2893974488 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 · 2025-05-20T11:35:10Z

Test report by @boegelbot
FAILED
Build succeeded for 0 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 3.9.21
See https://gist.github.com/boegelbot/6f8306debc79e12aa675cb58479e50e4 for a full test report.

boegel · 2025-05-20T16:17:10Z

Problems with test report should be fixed thanks to changes in:

define $CONDA_PREFIX via modextravars in QIIME2 #22918

boegel · 2025-05-20T16:17:19Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-20T16:20:08Z

@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=22904 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22904 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6403

Test results coming soon (I hope)...

Details

- notification for comment with ID 2895083986 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 · 2025-05-20T16:59:59Z

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 3.9.21
See https://gist.github.com/boegelbot/e85b8830ac0cccd15988ed62f60313b6 for a full test report.

add CONDA_PREFIX only for unifrac

pavelToman · 2025-05-20T17:13:32Z

I made the same changes as @boegel in cc976f6

pavelToman · 2025-05-20T17:13:37Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-20T17:20:08Z

@pavelToman: 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=22904 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22904 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6405

Test results coming soon (I hope)...

Details

- notification for comment with ID 2895241427 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 · 2025-05-20T17:56:34Z

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 3.9.21
See https://gist.github.com/boegelbot/e85b776f2f257fef110e0836b282ffff for a full test report.

boegel · 2025-05-20T18:02:38Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3505.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/132f55a268c09dee2b1168bb33b639cf for a full test report.

boegel

lgtm

boegel · 2025-05-20T18:13:14Z

Going in, thanks @pavelToman!

pavelToman · 2025-05-20T19:43:07Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4004.donphan.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 570.86.15, Python 3.9.18
See https://gist.github.com/pavelToman/7e90cd5fe1a66abdd644ddf2e651b164 for a full test report.

Compatible qiime2 version for foss/2023a

8db552d

pavelToman added the update label May 16, 2025

pavelToman mentioned this pull request May 16, 2025

QIIME2 vscentrum/vsc-software-stack#521

Closed

2 tasks

pavelToman changed the title ~~Compatible qiime2 version for foss/2023a~~ QIIME2-2024.2.0-foss-2023a - compatible qiime2 version for foss/2023a + delete QIIME2-2024.10.1-foss-2023a May 16, 2025

pavelToman and others added 2 commits May 16, 2025 11:58

Delete easybuild/easyconfigs/q/QIIME2/QIIME2-2024.10.1-foss-2023a-amp…

3d39946

…licon.eb

add patch for v2024.2.0

1cb4b93

github-actions Bot added change and removed update labels May 16, 2025

boegel self-assigned this May 20, 2025

Merge branch 'develop' into 20250516115358_new_pr_QIIME2202420

8e5120c

boegel added the bug fix label May 20, 2025

boegel added this to the next release (5.0.1 or 5.1.0) milestone May 20, 2025

boegel changed the title ~~QIIME2-2024.2.0-foss-2023a - compatible qiime2 version for foss/2023a + delete QIIME2-2024.10.1-foss-2023a~~ stick to QIIME2 2024.2.0 with foss/2023a, since recent versions (like 2024.10.0) require a more recent version of pandas May 20, 2025

Update QIIME2-2024.2.0-foss-2023a-amplicon.eb

29644a9

add CONDA_PREFIX only for unifrac

boegel approved these changes May 20, 2025

View reviewed changes

boegel merged commit f8b0092 into easybuilders:develop May 20, 2025
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