Add file to easily run BiG-SCAPE using a docker image (single use)

run_bigscape

+#!/bin/bash
+
+if [[ $# -eq 0 ||  $1 == "-h" ||  $1 == "--help" ]]; then
+	docker run \
+	--detach=false \
+	--rm \
+	--user=$(id -u):$(id -g) \
+	docker-registry.wur.nl/medema-group/big-scape \
+    	$@
+else
+	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)
+	echo input ${INPUT_FILE}
+	readonly INPUT_DIR=$(dirname $(realpath $1))
+	shift
+
+
+	# handle output file
+	if [[ $# -eq 0 ]]; then
+		echo You must specify an output dir
+		exit 1;
+	else
+		readonly OUTPUT_FILE=$(basename $1)
+		echo output ${OUTPUT_FILE}
+		readonly OUTPUT_DIR=$(dirname $(realpath $1))
+		shift
+	fi
+
+	if [ ! -d ${OUTPUT_DIR} ]; then
+   		mkdir ${OUTPUT_DIR}
+	fi
+
+	# Links within the container
+	readonly CONTAINER_SRC_DIR=/home/input
+	readonly CONTAINER_DST_DIR=/home/output
+
+
+	#if [ ${INPUT_FILE} ${OUTPUT_FILE} ]; then
+	if [ ! -z ${INPUT_FILE} ] && [ ! -z ${OUTPUT_FILE} ]; then
+		echo bigscape is running now
+		docker run \
+	    	--volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:ro \
+	    	--volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
+	    	--detach=false \
+	    	--rm \
+	    	--user=$(id -u):$(id -g) \
+	    	docker-registry.wur.nl/medema-group/big-scape\
+	    	-i ${CONTAINER_SRC_DIR}/${INPUT_FILE} \
+	    	-o ${CONTAINER_DST_DIR}/${OUTPUT_FILE}\
+    		$@
+	fi
+fi