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BIC-MNI / minc-toolkit-v2

Version 2 of the minc-toolkit, uses tools based on ITK version 4.x
GNU General Public License v3.0
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Container QoL #129

Open jordandekraker opened 3 years ago

jordandekraker commented 3 years ago

Just a minor suggestion to improve quality of living when using singularity or docker:

Currently pulling the container docker://nistmni/minc-toolkit:1.9.16 works great, except all programs must be run with /opt/min/1.9.16/bin/. For example singularity exec minc-toolkit_1.9.16.sif /opt/min/1.9.16/bin/nii2mnc correctly returns the usage for this executable.

Simply adding the following line to the Dockerfile and rebuilding the container would make this much easier to use: ENV PATH /opt/min/1.9.16/bin:$PATH. The above command would now be singularity exec minc-toolkit_1.9.16.sif nii2mnc

Thanks!

vfonov commented 3 years ago

Like this: https://github.com/vfonov/minc-toolkit-containers/blob/master/singularity/Singularity.1.9.16#L62 ?

jordandekraker commented 3 years ago

Looks like that would do it! I guess I just needed to pull the latest image.

Perhaps that could be updated in the documentation? e.g. docker pull nistmni/minc-toolkit:1.9.16 could be changed to docker pull nistmni/minc-toolkit:latest assuming that this would only be stable releases.

Thanks for the speedy response!