#!/bin/sh

usage() {
    echo "Usage: $0 -output OUTPUTDIR -ref REF -draft DRAFT"
    exit 1
}

if ! echo $* | grep -- -output ; then
    echo "Missing output dir specified by '-output DIR' ."
    usage
fi
if ! echo $* | grep -- -ref ; then
    echo "Missing reference specified by '-ref REF' ."
    usage
fi
if ! echo $* | grep -- -draft ; then
    echo "Missing draft genome specified by '-draft DRAFT' ."
    usage
fi

java -Xmx6g -cp /usr/share/java/Mauve.jar org.gel.mauve.contigs.ContigOrderer $*
