#!/bin/bash
#SBATCH -p medium
#SBATCH -N 1
#SBATCH -t 60:00

module load singularity

singularity run /sw/tools/singularity/lolcow.sif

Binding directories

Sometimes it is required to have some specific paths in container, which are not mounted by default. For instance, /scratch/tmp is a default TMPDIR in the host system and is not available by default within the container, which might cause problems with software that needs it. You can either edit the environment variable or bind the /scratch as shown below:

singularity {run|exec|shell} --bind /scratch /path/to/singularity.sif