{bio}[system/system] FSL v6.0.7.11 by pavelToman · Pull Request #25383 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-02-23T12:00:24Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#640
requires:

update Conda easyblock to take into account that in Conda 24.3 --force was renamed to --yes easybuild-easyblocks#3573

pavelToman · 2026-02-23T12:02:30Z

@boegelbot please test @ jsc-zen3 EB_ARGS="--include-easyblocks-from-pr 3573"

boegelbot · 2026-02-23T12:10:10Z

@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=25383 EB_ARGS="--include-easyblocks-from-pr 3573" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25383 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9810

Test results coming soon (I hope)...

Details

- notification for comment with ID 3944361010 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 · 2026-02-23T12:25:57Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
FAILED
Build succeeded for 0 out of 1 (total: 15 mins 26 secs) (1 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/5c2c667992336ab3c91b34e0565926b9 for a full test report.

pavelToman · 2026-02-24T10:37:39Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/ecpr-22914 --include-easyblocks-from-pr=3573"

Gonna fail, I forgot to change PR number

boegelbot · 2026-02-24T10:40:07Z

@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=25383 EB_ARGS="--installpath /tmp/$USER/ecpr-22914 --include-easyblocks-from-pr=3573" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25383 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9826

Test results coming soon (I hope)...

Details

- notification for comment with ID 3950733740 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 · 2026-02-24T10:43:17Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
FAILED
Build succeeded for 0 out of 1 (total: 42 secs) (1 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/81354fb2a6cf1a6e802c73594fb8a63d for a full test report.

pavelToman · 2026-02-24T10:46:42Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr=3573"

pavelToman · 2026-02-24T10:47:23Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 14 mins 3 secs) (1 easyconfigs in total)
node4012.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/73c3b4434eea181820ed490f113899fd for a full test report.

boegelbot · 2026-02-24T10:50:09Z

@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=25383 EB_ARGS="--include-easyblocks-from-pr=3573" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25383 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9828

Test results coming soon (I hope)...

Details

- notification for comment with ID 3950791691 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).

pavelToman · 2026-02-24T10:52:24Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 13 mins 21 secs) (1 easyconfigs in total)
node4203.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/b2af09f37cf4015cc4f9f7d7a9040795 for a full test report.

pavelToman · 2026-02-24T11:06:26Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 14 mins 1 secs) (1 easyconfigs in total)
node4012.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/e4c1f24397951d1bac206774ac091a43 for a full test report.

boegelbot · 2026-02-24T11:07:17Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 16 mins 50 secs) (1 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/6006db6110496273de4fb54295cc66a3 for a full test report.

laraPPr · 2026-04-01T13:50:05Z

Test report by @laraPPr
FAILED
Build succeeded for 0 out of 1 (total: 13 secs) (1 easyconfigs in total)
node4239.shinx.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/laraPPr/267b4b11910aa7b3f4c54437bf01ab1f for a full test report.

laraPPr · 2026-04-01T14:02:30Z

Test report by @laraPPr FAILED Build succeeded for 0 out of 1 (total: 13 secs) (1 easyconfigs in total) node4239.shinx.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21 See https://gist.github.com/laraPPr/267b4b11910aa7b3f4c54437bf01ab1f for a full test report.

@pavel I rebuild MiniForge with easybuilders/easybuild-easyblocks#3573 but it still fails with

conda: error: unrecognized arguments: --force

pavelToman · 2026-04-01T14:29:32Z

Test report by @laraPPr FAILED Build succeeded for 0 out of 1 (total: 13 secs) (1 easyconfigs in total) node4239.shinx.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21 See https://gist.github.com/laraPPr/267b4b11910aa7b3f4c54437bf01ab1f for a full test report.

@pavel I rebuild MiniForge with easybuilders/easybuild-easyblocks#3573 but it still fails with
conda: error: unrecognized arguments: --force

FSL needs this update to conda easyblock too

laraPPr · 2026-04-01T14:50:06Z

Test report by @laraPPr
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 17 mins 47 secs) (1 easyconfigs in total)
node4239.shinx.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/laraPPr/fbdf6f306c012d934ba56b9b94ab59c0 for a full test report.

boegel · 2026-04-08T18:24:42Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 2 out of 2 (total: 15 mins 8 secs) (1 easyconfigs in total)
node4211.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/5fb145d62c3f77bb1b3f6ccc2656afee for a full test report.

boegel

lgtm

boegel · 2026-04-08T18:37:42Z

Going in, thanks @pavelToman!

adding easyconfigs: FSL-6.0.7.11.eb

d4bdec7

pavelToman added the update label Feb 23, 2026

pavelToman mentioned this pull request Feb 23, 2026

FreeSurfer 7.4.1 and FSL 6.0.7.11 vscentrum/vsc-software-stack#640

Open

2 tasks

github-actions Bot added new and removed update labels Feb 23, 2026

Update FSL-6.0.7.11.eb

b186511

pavelToman mentioned this pull request Feb 24, 2026

{bio}[system/system] FSL v6.0.7.17 #22914

Merged

1 task

pavelToman mentioned this pull request Feb 24, 2026

update Conda easyblock to take into account that in Conda 24.3 --force was renamed to --yes easybuilders/easybuild-easyblocks#3573

Merged

Update FSL-6.0.7.11.eb

a834ea6

boegel assigned laraPPr Mar 9, 2026

Merge branch 'easybuilders:develop' into 20260223130020_new_pr_FSL60711

48ea6bc

boegel approved these changes Apr 8, 2026

View reviewed changes

boegel added this to the next release (5.3.0) milestone Apr 8, 2026

boegel merged commit b63e513 into easybuilders:develop Apr 8, 2026
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