#!/bin/bash
# Wrapper scripts that sets --jar gridss.jar command line argument
# so users don't need to know the path to the GRIDSS jar

# Adapted from bioconda-recipes/picard/picard.sh
set -o pipefail
# Find original directory of bash script, resolving symlinks
# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
    SOURCE="$(readlink "$SOURCE")"
    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

$DIR/$(basename $0)  --jar "$DIR/gridss.jar" "$@"