One other note is that I noticed the documentation for Singularity containers appears to be different on the ‘Installation’ and ‘Usage’ pages. Is one of these more correct? I built the container using the ‘installation’ instructions (i.e. created a .sif, not .simg). Thanks so much!
The easiest way to get a Sigularity image is to run:
$ singularity build qsiprep-.sif docker://pennbbl/qsiprep:
Using qsiprep within a singularity container (qsiprep-.simg)
To run qsiprep with singularity, a singularity image must be built (see Installation). This is the preferred method for HPCs. For example
$ singularity run --cleanenv -B /data/:/home/$user/data qsiprep-.simg