Run AS5 RC in Docker

run_as5rc1.sh

#!/bin/bash

set -o errexit
set -o nounset


# handle input file
readonly INPUT_FILE=$(basename $1)
readonly INPUT_DIR=$(dirname $(readlink -f $1))
shift

# handle output file
readonly OUTPUT_DIR=$(readlink -f $1)
shift

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

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

docker run \
    --volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:ro \
    --volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
    --detach=false \
    --rm \
    --user=$(id -u):$(id -g) \
    antismash/standalone:5.0.0rc1 \
    ${INPUT_FILE} \
    $@