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Allow for setting to map PWD into consistent path inside container #63

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yarikoptic opened this issue Dec 10, 2021 · 0 comments
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https://github.com/ReproNim/containers/blob/master/scripts/singularity_cmd#L101

SARGS=( -e -B "$PWD" -H "$BHOME" --pwd "$PWD" "$@" )

Usecase came from fmriprep and alerted to by @satra : for any sizeable dataset we need first to "bootstrap" pybids DB using smth like (thanks @smeisler):

pybids layout --index-metadata --reset-db $bids_dir $database_outdir

and pass that location to fmriprep via bids-database-dir.

I even wonder if such mode of operation should be a default one, and default e.g. to /tmp ?

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