minify doesn't work as expected

[sooyounga]

while working on #408, we ran into minify issue where mri_convert was not found after minify-ing we verified mri_convert is working before minify-ing

commands used:

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:buster-slim \
    --freesurfer version=7.1.1 \
> freesurfer7.Dockerfile

docker build --tag freesurfer:7.1.1 --file freesurfer7.Dockerfile .

cmd1="mri_convert /home/T1.nii.gz /home/T1.mgz"
cmd2="mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2"

docker run --rm -itd \
    --name fs \
    --security-opt=seccomp:unconfined \
    -v ${PWD}:/home \
    -v ${PWD}/freesurfer_license.txt:/opt/freesurfer-7.1.1/license.txt \
    -e FS_LICENSE="/opt/freesurfer-7.1.1/license.txt" \
    freesurfer:7.1.1

neurodocker minify \
    --container fs \
    --dir /opt/freesurfer-7.1.1/ \
    "$cmd1" "$cmd2"

[kaczmarj]

hi @sooyounga - does the file /opt/freesurfer-7.1.1/bin/mri_convert exist in the minified container?

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[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity.