cat12-container/code/main

#!/bin/bash

# Help

if [ "$#" = 0 ]
then
    echo "ERROR: No arguments passed."
    cat /.singularity.d/runscript.help
    exit 1
fi

# Copy or view batch files

STANDALONE="/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/standalone"

if [ "$1" = "copy" ]
then
    if [ "$2" = "all" ]
    then
	echo "Copying batch files to:"
	cp -vi ${STANDALONE}/*.txt "$3"
	exit 0
    elif [ -f ${STANDALONE}/"$2" ]
    then
	echo "Copying batch file to:"    
	cp -vi ${STANDALONE}/"$2" "$3"
	exit 0
    else
	echo "ERROR: batch file $2 not found. Available batch files are:"
	find ${STANDALONE} -name "*.txt" -printf "%f\n"
	exit 1
    fi
elif [ "$1" = "view" ]
then
    if [ -f ${STANDALONE}/"$2" ]
    then
	cat ${STANDALONE}/"$2"
	exit 0
    else
        echo "ERROR: batch file $2 not found. Available batch files are:"
        find ${STANDALONE} -name "*.txt" -printf "%f\n"
        exit 1
    fi
fi

# Run CAT

NOW=$(date +%s)
exec /code/cat_standalone.sh "$@" 2>&1 |tee cat_$NOW.log