ChromHMM.sh

#!/bin/bash

# Wraps ChromHMM.jar
#
# This is copied from https://github.com/chapmanb/gatk
#
set -o pipefail

# Find original directory of bash script, resovling 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 )"

JAR_DIR=$DIR
java=java
if [ -e "$JAVA_HOME/bin/java" ]
then
java="$JAVA_HOME/bin/java"
fi

# extract memory and system property Java arguments from the list of provided arguments
# http://java.dzone.com/articles/better-java-shell-script
default_jvm_mem_opts="-Xms512m -Xmx1g"
jvm_mem_opts=""
jvm_prop_opts=""
pass_args=""
for arg in "$@"; do
    case $arg in
        '-D'*)
            jvm_prop_opts="$jvm_prop_opts $arg"
            ;;
        '-XX'*)
            jvm_prop_opts="$jvm_prop_opts $arg"
            ;;
         '-Xm'*)
            jvm_mem_opts="$jvm_mem_opts $arg"
            ;;
         *)
            pass_args="$pass_args $arg"
            ;;
    esac
done

if [ "$jvm_mem_opts" == "" ]; then
    jvm_mem_opts="$default_jvm_mem_opts"
fi

pass_arr=($pass_args)
if [[ ${pass_arr[0]} == org* ]]
then
    eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/ChromHMM.jar" $pass_args
else
    eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/ChromHMM.jar" $pass_args
fi
exit