Currently, all environments are set up in /home/pnlbwh/.bashrc through a bunch of source. That way, we didn't have to explicitly define variables like CONDA_PREFIX. This shortcut puts an overhead on the user about providing any command to run within " " such as:
docker run --rm tbillah/pnlpipe "nifti_atlas --help"
Currently, all environments are set up in
/home/pnlbwh/.bashrcthrough a bunch ofsource. That way, we didn't have to explicitly define variables likeCONDA_PREFIX. This shortcut puts an overhead on the user about providing any command to run within" "such as:However, if singularity like environment definition is used, we should not have to enclose within
" ": https://github.com/pnlbwh/pnlpipe-containers/blob/master/Singularity.pnlpipe#L88Impact of the overhead should be minor because not a lot of users may have docker capability. But we should fix it in the future.