Small fixes to shell scripts #553
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This PR does not pass checks because sphinx 8 somehow treats importing of files different to sphinx 7. This needs to be debugged at some point, but we should just use sphinx 7 for now. The limitation to sphinx 7 is implemented in #552, so this PR's checks should rerun and be merged after merging #552. |
…_dir is set, is root, is writable) Bump tqdm to 4.66 (has no effect on results) add BATCH documentation (brun_fastsurfer.sh usage docs and TQDM_DISABLE=1 doc) Add --env TQDM_DISABLE=1 for slurm running to pollute the logs less Fix the parsing of subjects in brun_fastsurfer.sh Clean up the parameter parsing and fix some minor Shellshock Warning in srun_fastsurfer.sh
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Add a checking for subjects_dir to run_fastsurfer.sh (whether subject_dir is set, is root, is writable)
Bump tqdm to 4.66 (has no effect on results)
add BATCH documentation (brun_fastsurfer.sh usage docs and TQDM_DISABLE=1 doc) Add --env TQDM_DISABLE=1 for slurm running to pollute the logs less Fix the parsing of subjects in brun_fastsurfer.sh
Clean up the parameter parsing and fix some minor Shellshock Warning in srun_fastsurfer.sh