patching singularity containers

[jdkent]

In the current contributors.rst, it says to use the PYTHONPATH variable to patch singularity containers.

Patching containers can be achieved in Singularity by using the PYTHONPATH variable:

$ PYTHONPATH="$HOME/projects/fmriprep" singularity run fmriprep.img \
     /scratch/dataset /scratch/out participant -w /out/work/

This method did not work for me (but I didn't try hard to make it work). However binding did work, and it's synonymous with how we patch with docker containers.

e.g.

singularity run \
-B $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6/site-packages/fmriprep \
fmriprep.img \
/scratch/dataset /scratch/out participant -w /out/work/

This would be my preferred way of patching singularity containers, but I want to get other opinions before opening up a pull request to change the docs.

[oesteban]

+1 to update the guide and place your method 1st (although keeping the PYTHONPATH mechanism)