{bio}[system/system] FSL v6.0.7.17 by sassy-crick · Pull Request #22914 · easybuilders/easybuild-easyconfigs

sassy-crick · 2025-05-19T14:01:41Z

(created using eb --new-pr)

Requires:

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

github-actions · 2025-05-19T14:02:06Z

Updated software `FSL-6.0.7.17.eb`

Diff against FSL-6.0.5.1-foss-2021a.eb

easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb

diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.7.17.eb
index 749b5cf34a..07321d466d 100644
--- a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb
+++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.7.17.eb
@@ -1,87 +1,35 @@
-# This build still relies on the following libraries (or part of them) shipped with FSL:
-#    GDCHART, libprob, libcprob, cprob, newran, newmat
-# Attempts to use externally built libraries failed. Worth trying again in the future...
-#
-# Added fslpy 3.5.3, which provides tools like imcp and imglob
+easyblock = 'Conda'
 
 name = 'FSL'
-version = '6.0.5.1'
+version = '6.0.7.17'
 
 homepage = 'https://www.fmrib.ox.ac.uk/fsl/'
 description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
-toolchainopts = {'cstd': 'c++11'}
+source_urls = ['https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/']
+sources = ['fsl-%(version)s_linux-64.yml']
+checksums = ['42892113183166822d114fcda6607c2da073c561dd3b5b59589f9433b95e0ed8']
 
-source_urls = ['https://www.fmrib.ox.ac.uk/fsldownloads/']
-sources = ['%(namelower)s-%(version)s-sources.tar.gz']
-patches = [
-    'FSL-6.0.4_Makefile_fixes.patch',
-    'FSL-6.0.5.1_disable_cuda.patch',
-    'FSL-6.0.4_build_fixes.patch',
-    'FSL-6.0.2_Build_extras.patch',
-    'FSL-6.0.1_Fix_fsl_exec_script.patch',
-    'FSL-6.0.5.1_fix-cprob-include.patch',
-    'FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch',
-]
-checksums = [
-    'd8ab2ebc87d3e33ce1097dde18d8a55f62d4a27b45efc4f68adccfb6e8e1425c',  # fsl-6.0.5.1-sources.tar.gz
-    '43217e86e715a149ec27dfad471383e8f142863aa6f3f943ab4db379bc851055',  # FSL-6.0.4_Makefile_fixes.patch
-    'a1e844507207567b7a1df19b484d66b8b30194e455123b78cfd05e236ed864fb',  # FSL-6.0.5.1_disable_cuda.patch
-    '1bc83cfeffff21a68db47b6929e94634fc8aaf3db8e276e160e3f468f0889000',  # FSL-6.0.4_build_fixes.patch
-    '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5',  # FSL-6.0.2_Build_extras.patch
-    'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef',  # FSL-6.0.1_Fix_fsl_exec_script.patch
-    '6c06d92979bf5ef4c24d71fc459a230017398a8124cfa253cbc0556a6cf2d420',  # FSL-6.0.5.1_fix-cprob-include.patch
-    '0bee00eb136d3431fa7332aac7957b1c90bc93c381ecc6379d93e19a933ac4bc',  # FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch
-]
+toolchain = SYSTEM
 
-dependencies = [
-    ('Python', '3.9.5'),
-    ('Boost', '1.76.0'),
-    ('libgd', '2.3.1'),
-    ('libxml2', '2.9.10'),
-    ('libxml++', '2.42.1'),
-    ('SQLite', '3.35.4'),
-    ('libpng', '1.6.37'),
-    ('Tk', '8.6.11'),
-    ('NLopt', '2.7.0'),
-    ('freeglut', '3.2.1'),
-    ('expat', '2.2.9'),
-    ('zlib', '1.2.11'),
-    ('VTK', '9.0.1'),
-    ('GSL', '2.7'),
-    ('Qwt', '6.2.0'),
-    ('h5py', '3.2.1'),
-    ('NiBabel', '3.2.1'),
-]
+builddependencies = [('Miniforge3', '24.11.3-0')]
 
-exts_defaultclass = 'PythonPackage'
+environment_file = 'fsl-%(version)s_linux-64.yml'
 
-exts_default_options = {
-    'source_urls': [PYPI_LOWER_SOURCE],
+sanity_check_paths = {
+    'files': ['bin/flirt', 'bin/fsl', 'bin/fslpython', 'bin/imcp', 'bin/fsl_sub', 'lib/libfsl-surface.%s' % SHLIB_EXT],
+    'dirs': ['include/fslsurface', 'lib/python3.12/site-packages'],
 }
 
-exts_list = [
-    ('dataclasses', '0.8', {
-        'checksums': ['8479067f342acf957dc82ec415d355ab5edb7e7646b90dc6e2fd1d96ad084c97'],
-        'preinstallopts': "sed -i '/python_requires/d' setup.py && ",
-    }),
-    # The executable files 'imglob' and 'imcp' come from fslpy
-    ('fslpy', '3.5.3', {
-        'checksums': ['f80ef8b7b49f475bfb71946619d33c118a7cbbe106c72f7777aaf14d9e261530'],
-        'installopts': '--prefix=%(installdir)s/fsl',
-    }),
+sanity_check_commands = [
+    "source $FSLDIR/etc/fslconf/fsl.sh && fslpython --help",
+    "python -c 'import fsl'",
 ]
 
-modextrapaths = {
-    'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages'],
-}
-
 modextravars = {
-    'FSLOUTPUTTYPE': 'NIFTI_GZ',
-    'FSLMULTIFILEQUIT': 'TRUE',
-    'FSLTCLSH': 'tclsh',
-    'FSLWISH': 'wish8.6',
+    'FSLDIR': '%(installdir)s',
 }
 
+modloadmsg = "To start using FSL, first run 'source $FSLDIR/etc/fslconf/fsl.sh'"
+
 moduleclass = 'bio'

sassy-crick · 2025-05-19T14:22:02Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-05-19T14:30:09Z

@sassy-crick: 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=22914 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22914 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6390

Test results coming soon (I hope)...

Details

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boegelbot · 2025-05-19T14:59:16Z

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/1214b1e18c4bae5359e1ff30a06aad0c for a full test report.

verdurin · 2025-05-27T16:43:19Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (1 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 3.11.11
See https://gist.github.com/verdurin/b1afe32682de5ef25ea72871b8eed15b for a full test report.

boegel · 2025-06-16T16:07:28Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-06-16T16:10:13Z

@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=22914 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22914 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6793

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
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boegelbot · 2025-06-16T16:13:22Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c4.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/84642888c35fa420f9fe7b41aae468e8 for a full test report.

boegel · 2025-06-16T16:22:35Z

Hmm, this looks fishy:

conda: error: unrecognized arguments: --force

@verdurin Any idea if this could be caused by using Miniforge3 as you suggested?

sassy-crick · 2025-06-17T13:49:55Z

Hmm, this looks fishy:
conda: error: unrecognized arguments: --force
@verdurin Any idea if this could be caused by using Miniforge3 as you suggested?

I had a look into that already and indeed, the --force is not recognised in the suggested Miniforge3. So either we update the Conda EasyBlock accordingly, which is something I was thinking of and started to look into that, or we create a new EasyBlock. Personally, I am in favour of the first option.

verdurin · 2025-08-12T11:09:03Z

Would be happy to test the modified easyblock if you want to make a start.

Thyre · 2026-01-19T10:08:18Z

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

boegelbot · 2026-01-19T10:10:09Z

@Thyre: 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=22914 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_22914 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9418

Test results coming soon (I hope)...

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boegelbot · 2026-01-19T10:34:19Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 23 mins 53 secs) (1 easyconfigs in total)
jsczen3c2.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/3368b9c2e813bf8a9766e30e1c1bf798 for a full test report.

verdurin · 2026-02-16T11:47:32Z

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (total: 2 mins 0 secs) (1 easyconfigs in total)
centos-stream-9 - Linux CentOS Stream 9, x86_64, Intel Core Processor (Skylake, IBRS), Python 3.12.12
See https://gist.github.com/verdurin/e79e6d7bf363bf064a43d392a62099f0 for a full test report.

verdurin · 2026-02-16T11:48:44Z

@sassy-crick still seeing the error:

usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
conda: error: unrecognized arguments: --force

Thyre · 2026-02-16T12:18:28Z

@sassy-crick still seeing the error:


usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...

conda: error: unrecognized arguments: --force

@verdurin, this needs easybuilders/easybuild-easyblocks#3573
@sassy-crick Can you add this dependency to the PR description?

sassy-crick · 2026-02-16T12:36:13Z

@sassy-crick still seeing the error:
usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...

conda: error: unrecognized arguments: --force
@verdurin, this needs easybuilders/easybuild-easyblocks#3573 @sassy-crick Can you add this dependency to the PR description?

Done. I was working on that already, but wanted to test it before I update it.

pavelToman · 2026-02-20T12:14:53Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 2 out of 2 (total: 16 mins 24 secs) (1 easyconfigs in total)
node4010.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/1a2ed9333ae2b4b083602e360295a0bc for a full test report.

pavelToman · 2026-02-20T12:48:32Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 2 out of 2 (total: 14 mins 19 secs) (1 easyconfigs in total)
node4205.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/01649db53a8ad7feec31ec6967966f16 for a full test report.

pavelToman · 2026-02-24T10:37:27Z

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

Gonna fail, run also #25383 with the same installpath accidentally

boegelbot · 2026-02-24T10:40:11Z

@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=22914 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_22914 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9827

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
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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/324bd8d487cb00a7cd9f2f502af2e63b for a full test report.

pavelToman · 2026-02-24T10:45:30Z

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

boegelbot · 2026-02-24T10:50:12Z

@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=22914 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_22914 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9829

Test results coming soon (I hope)...

Details

- notification for comment with ID 3950783298 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 · 2026-02-24T11:07:26Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 17 mins 0 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/0c82c5d14f6b462adccf0f2e06e114ff for a full test report.

pavelToman · 2026-02-24T11:23:38Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 14 mins 30 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/8e27438a9bd4c003f4d31d952f8d36b1 for a full test report.

boegel

lgtm

boegel · 2026-04-08T18:37:37Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3573
SUCCESS
Build succeeded for 1 out of 1 (total: 12 mins 12 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/795965cdbd05d5ba54d0d7596985e804 for a full test report.

boegel · 2026-04-08T18:38:02Z

Going in, thanks @sassy-crick!

adding easyconfigs: FSL-6.0.7.17.eb

6ed7c8d

sassy-crick added the update label May 19, 2025

verdurin reviewed May 27, 2025

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Comment thread easybuild/easyconfigs/f/FSL/FSL-6.0.7.17.eb Outdated

boegel mentioned this pull request Jun 16, 2025

{bio}[system/system] FSL v6.0.7.2 #18697

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boegel requested changes Jun 16, 2025

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Comment thread easybuild/easyconfigs/f/FSL/FSL-6.0.7.17.eb Outdated

use Miniforge3 as build dependency for FSL 6.0.7.17

5769ab1

sassy-crick added the ready-to-review label Feb 16, 2026

pavelToman mentioned this pull request Feb 19, 2026

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

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2 tasks

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

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boegel approved these changes Apr 8, 2026

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

boegel merged commit 318903d into easybuilders:develop Apr 8, 2026
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