Provide a docker/singularity container and use it as a $COMMAND_PREFIX wrapper

[gdevenyi]

I believe we can achieve runtime containerization of the pipeline by adding a $COMMAND_PREFIX to the front of every command like so:

${COMMAND_PREFIX} antsRegistration_affine_SyN.sh <other options>

Where for bare-metal runs ${COMMAND_PREFIX} is an empty string, but we can also provide a container:

COMMAND_PREFIX='singularity exec containerfile.sif'

Which we can publish along with the pipeline.