protpipe.sh

#!/usr/bin/env bash

#### CHECK SINGULARITY #############################################################################
if ! command -v singularity &> /dev/null; then
    echo "INFO: singularity command not found, looking for singularity module"
    if ! command -v module &> /dev/null; then
        echo "ERROR: module command not found. Did you mean to run this on an HPC?"
        exit 1
    else
        if $(module avail singularity 2>&1 >/dev/null | grep -q 'No module'); then
            echo 'ERROR: singularity cannot be found. Recheck installation?'
            exit 1
        else
            echo 'INFO: module singularity found'
            module load singularity
        fi
    fi
else
    echo 'INFO: singularity command found'
fi


#### R ANALYSIS ####################################################################################
r_sif="src/R.sif"
# r_sif_sha256_desired='91c7e63ed529a50455e810a7911424b71b62a05180eab4db93f3d172a6788ee7'
if [ ! -f "${r_sif}" ]; then
    echo "INFO: pulling image from quay.io"
    singularity pull src/R.sif docker://quay.io/datatecnica/protpipe:latest
else
    echo "INFO: ${r_sif} already exists, skipping download"
fi

#r_sif_sha256_actual=$(sha256sum "${r_sif}" | awk '{print $1}')

#if [ ! "${r_sif_sha256_actual}" == "${r_sif_sha256_desired}" ]; then
#    echo "ERROR: ${r_sif} sha256sum does not pass check. Possibly corrupted? Delete or clear singularity cache and try again."
#    exit 1
#else
#    echo "INFO: ${r_sif} sha256sum sum passes check"
#fi

#### RUN IN CONTAINER ####################################################################################

if [ $# -eq 0  ]; then
    echo -e "No arguments provided--exiting"
    exit 0
elif [ "${1}" == 'R' ]; then
    echo 'INFO: starting interactive R session'
    singularity exec --cleanenv -H ${PWD} ${r_sif} R
elif [ "${1}" == 'immuno' ]; then
    shift
    singularity exec --cleanenv -H ${PWD} ${r_sif} src/immunopeptidome.R $@
elif [ "${1}" == 'APMS' ]; then
    shift
    singularity exec --cleanenv -H ${PWD} ${r_sif} src/APMS.R $@
elif [ "${1}" == 'basic' ]; then
    shift
    singularity exec --cleanenv -H ${PWD} ${r_sif} src/basic_analysis.R $@
else
    echo -e "Check first argument and try again."
    echo -e "Valid first arguments include one of the following:"
    echo -e "    R         (start containerized interactive R session)"
    echo -e "    basic     (differential abundance and enrichment analysis of standard MS data)"
    echo -e "    APMS      (for Affinity Purification Mass Spec analysis)"
    echo -e "    immuno    (immunopeptidome MHC prediction)"
    echo -e "Provided Args: $@"
fi