Upload Nipype Image to Sherlock


I’ve been trying to upload an image containing Nipype docker container to Sherlock so that everyone in our lab can run the same version. Using vagrant virtual machine, I first created an image: “sudo singularity create --size 8000 nipype.img” and then imported Nipype docker container into this image: “sudo singularity import nipype.img docker://nipype/nipype:latest”. I then uploaded this image to Sherlock and ran it: “singularity run nipype.img” but I get the following error:

/.run: 35: export: /opt/mcr/v85/: bad variable name

I’d appreciate it if anyone could help solve this! If anyone has gone through these steps and already has an image on the cluster, it would be great if they could share. Thanks!


This is the relevant signularity bug report: https://github.com/singularityware/singularity/issues/719

Until this is resolved, you might have better luck using docker2singularity to create the singularity image.