An example script to run a Singularity container for a user on the list

singularity_example_bash.sh

#!/bin/bash

# Before you run this script, pull your container somewhere, and then provide
# the full path as an argument to this script
# If your $HOME is small, export to where you have more space like scratch
# export SINGULARITY_CACHEDIR=$SCRATCH/.singularity
# singularity pull --name antismash-standalone-4.2.0.sif docker://antismash/standalone:4.2.0
# Then provide the full container path as the last argument.

set -o errexit
set -o nounset

function realpath() {
    echo $(readlink -f $1 2>/dev/null || python -c "import sys; import os; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1)
}
 
# handle input file
readonly INPUT_FILE=$(basename $1)
readonly INPUT_DIR=$(dirname $(realpath $1))
shift

# Load singularity as module if you need to here, etc.
# module load singularity
 
# handle output file
readonly OUTPUT_DIR=$(realpath $1)
shift

# This is the container you pulled above, the full path, something like:
# $SCRATCH/.singularity/antismash-standalone-4.2.0.sif
CONTAINER_NAME=${1:-}
shift

if [ ! -f "${CONTAINER_NAME}" ]; then
    echo "$CONTAINER_NAME not found.";
    exit 1;
fi

# Links within the container
readonly CONTAINER_SRC_DIR=/input
readonly CONTAINER_DST_DIR=/output

if [ ! -d ${OUTPUT_DIR} ]; then
    mkdir ${OUTPUT_DIR}
fi

singularity run --bind ${INPUT_DIR}:${CONTAINER_SRC_DIR} --bind ${OUTPUT_DIR}:${CONTAINER_DST_DIR} "${CONTAINER_NAME}" "${@}"