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babs init did not include quotations around paths with wildcards #222

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tientong98 opened this issue Mar 19, 2025 · 0 comments · Fixed by #231
Open

babs init did not include quotations around paths with wildcards #222

tientong98 opened this issue Mar 19, 2025 · 0 comments · Fixed by #231
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bug Issues noting problems and PRs fixing those problems.

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@tientong98
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Currently, babs init did not include quotations around paths with wildcards. So within the singularity run cmd, it was -B /path/to/file/*.json instead of '-B /path/to/file/*.json'.

This lead to this error of lean dataset required to detect changes from command; use datalad status to inspect unsaved changes

I'm in /orcd/scratch/bcs/001/yibei/fs_bidsapp_babs/fs_bidsapp/analysis using /nfs/home2/yibei/micromamba/envs/simple2/bin/python
install(ok): /orcd/scratch/bcs/001/yibei/freesurfer_compute/job-64457467-sub-0026001/ds (dataset)
install(ok): /orcd/scratch/bcs/001/yibei/freesurfer_compute/job-64457467-sub-0026001/ds/inputs/data/BIDS (dataset) [Installed subdataset in order to get /orcd/scratch/bcs/001/yibei/freesurfer_compute/job-64457467-sub-0026001/ds/inputs/data/BIDS/sub-0026001]
run(impossible): /orcd/scratch/bcs/001/yibei/freesurfer_compute/job-64457467-sub-0026001/ds (dataset) [clean dataset required to detect changes from command; use `datalad status` to inspect unsaved changes]
@tientong98 tientong98 added the bug Issues noting problems and PRs fixing those problems. label Mar 19, 2025
@tientong98 tientong98 linked a pull request Mar 21, 2025 that will close this issue
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