#!/bin/sh
# ----------------------------------------------------------------------------
#  Copyright 2001-2006 The Apache Software Foundation.
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#       http://www.apache.org/licenses/LICENSE-2.0
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
# ----------------------------------------------------------------------------
#
#   Copyright (c) 2001-2006 The Apache Software Foundation.  All rights
#   reserved.


# resolve links - $0 may be a softlink
PRG="$0"

while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done

PRGDIR=`dirname "$PRG"`
BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`

# Reset the REPO variable. If you need to influence this use the environment setup file.
REPO=


# OS specific support.  $var _must_ be set to either true or false.
cygwin=false;
darwin=false;
case "`uname`" in
  CYGWIN*) cygwin=true ;;
  Darwin*) darwin=true
           if [ -z "$JAVA_VERSION" ] ; then
             JAVA_VERSION="CurrentJDK"
           else
             echo "Using Java version: $JAVA_VERSION"
           fi
		   if [ -z "$JAVA_HOME" ]; then
		      if [ -x "/usr/libexec/java_home" ]; then
			      JAVA_HOME=`/usr/libexec/java_home`
			  else
			      JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
			  fi
           fi       
           ;;
esac

if [ -z "$JAVA_HOME" ] ; then
  if [ -r /etc/gentoo-release ] ; then
    JAVA_HOME=`java-config --jre-home`
  fi
fi

# For Cygwin, ensure paths are in UNIX format before anything is touched
if $cygwin ; then
  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
fi

# If a specific java binary isn't specified search for the standard 'java' binary
if [ -z "$JAVACMD" ] ; then
  if [ -n "$JAVA_HOME"  ] ; then
    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
      # IBM's JDK on AIX uses strange locations for the executables
      JAVACMD="$JAVA_HOME/jre/sh/java"
    else
      JAVACMD="$JAVA_HOME/bin/java"
    fi
  else
    JAVACMD=`which java`
  fi
fi

if [ ! -x "$JAVACMD" ] ; then
  echo "Error: JAVA_HOME is not defined correctly." 1>&2
  echo "  We cannot execute $JAVACMD" 1>&2
  exit 1
fi

if [ -z "$REPO" ]
then
  REPO="$BASEDIR"/repo
fi

CLASSPATH="$BASEDIR"/etc:"$REPO"/commons-cli/commons-cli/1.2/commons-cli-1.2.jar:"$REPO"/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar:"$REPO"/commons-codec/commons-codec/1.4/commons-codec-1.4.jar:"$REPO"/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:"$REPO"/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:"$REPO"/org/tukaani/xz/1.0/xz-1.0.jar:"$REPO"/org/slf4j/slf4j-api/1.7.5/slf4j-api-1.7.5.jar:"$REPO"/log4j/log4j/1.2.17/log4j-1.2.17.jar:"$REPO"/org/xerial/snappy/snappy-java/1.1.1.6/snappy-java-1.1.1.6.jar:"$REPO"/org/bdgenomics/bdg-utils/bdg-utils-parquet/0.1.1/bdg-utils-parquet-0.1.1.jar:"$REPO"/com/twitter/parquet-avro/1.6.0rc4/parquet-avro-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-column/1.6.0rc4/parquet-column-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-common/1.6.0rc4/parquet-common-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-encoding/1.6.0rc4/parquet-encoding-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-generator/1.6.0rc4/parquet-generator-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-hadoop/1.6.0rc4/parquet-hadoop-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-jackson/1.6.0rc4/parquet-jackson-1.6.0rc4.jar:"$REPO"/com/twitter/parquet-format/2.2.0-rc1/parquet-format-2.2.0-rc1.jar:"$REPO"/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar:"$REPO"/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar:"$REPO"/org/bdgenomics/bdg-utils/bdg-utils-metrics/0.1.1/bdg-utils-metrics-0.1.1.jar:"$REPO"/org/bdgenomics/bdg-utils/bdg-utils-misc/0.1.1/bdg-utils-misc-0.1.1.jar:"$REPO"/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar:"$REPO"/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar:"$REPO"/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar:"$REPO"/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar:"$REPO"/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar:"$REPO"/org/apache/avro/avro/1.7.6/avro-1.7.6.jar:"$REPO"/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar:"$REPO"/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar:"$REPO"/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar:"$REPO"/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0.jar:"$REPO"/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar:"$REPO"/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar:"$REPO"/org/ow2/asm/asm/4.0/asm-4.0.jar:"$REPO"/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar:"$REPO"/org/objenesis/objenesis/1.2/objenesis-1.2.jar:"$REPO"/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar:"$REPO"/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar:"$REPO"/org/seqdoop/cofoja/1.1-r150/cofoja-1.1-r150.jar:"$REPO"/org/seqdoop/htsjdk/1.118/htsjdk-1.118.jar:"$REPO"/org/apache/ant/ant/1.8.2/ant-1.8.2.jar:"$REPO"/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar:"$REPO"/org/apache/bcel/bcel/5.2/bcel-5.2.jar:"$REPO"/jakarta-regexp/jakarta-regexp/1.4/jakarta-regexp-1.4.jar:"$REPO"/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:"$REPO"/org/testng/testng/6.8.8/testng-6.8.8.jar:"$REPO"/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar:"$REPO"/com/beust/jcommander/1.27/jcommander-1.27.jar:"$REPO"/com/google/guava/guava/14.0.1/guava-14.0.1.jar:"$REPO"/org/bdgenomics/adam/adam-apis/0.16.0/adam-apis-0.16.0.jar:"$REPO"/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar:"$REPO"/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar:"$REPO"/args4j/args4j/2.0.23/args4j-2.0.23.jar:"$REPO"/org/fusesource/scalate/scalate-core_2.10/1.6.1/scalate-core_2.10-1.6.1.jar:"$REPO"/org/fusesource/scalate/scalate-util_2.10/1.6.1/scalate-util_2.10-1.6.1.jar:"$REPO"/org/scala-lang/scala-compiler/2.10.0/scala-compiler-2.10.0.jar:"$REPO"/org/scalatra/scalatra-json_2.10/2.3.0/scalatra-json_2.10-2.3.0.jar:"$REPO"/org/json4s/json4s-core_2.10/3.2.10/json4s-core_2.10-3.2.10.jar:"$REPO"/org/json4s/json4s-ast_2.10/3.2.10/json4s-ast_2.10-3.2.10.jar:"$REPO"/org/scala-lang/scalap/2.10.0/scalap-2.10.0.jar:"$REPO"/org/scalatra/scalatra_2.10/2.3.0/scalatra_2.10-2.3.0.jar:"$REPO"/org/scalatra/scalatra-common_2.10/2.3.0/scalatra-common_2.10-2.3.0.jar:"$REPO"/org/clapper/grizzled-slf4j_2.10/1.0.2/grizzled-slf4j_2.10-1.0.2.jar:"$REPO"/org/scalatra/rl/rl_2.10/0.4.10/rl_2.10-0.4.10.jar:"$REPO"/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar:"$REPO"/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar:"$REPO"/joda-time/joda-time/2.3/joda-time-2.3.jar:"$REPO"/org/joda/joda-convert/1.6/joda-convert-1.6.jar:"$REPO"/org/scala-lang/scala-reflect/2.10.4/scala-reflect-2.10.4.jar:"$REPO"/org/bdgenomics/adam/adam-cli/0.16.0/adam-cli-0.16.0.jar

ENDORSED_DIR=
if [ -n "$ENDORSED_DIR" ] ; then
  CLASSPATH=$BASEDIR/$ENDORSED_DIR/*:$CLASSPATH
fi

if [ -n "$CLASSPATH_PREFIX" ] ; then
  CLASSPATH=$CLASSPATH_PREFIX:$CLASSPATH
fi

# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
fi

exec "$JAVACMD" $JAVA_OPTS  \
  -classpath "$CLASSPATH" \
  -Dapp.name="adam" \
  -Dapp.pid="$$" \
  -Dapp.repo="$REPO" \
  -Dapp.home="$BASEDIR" \
  -Dbasedir="$BASEDIR" \
  org.bdgenomics.adam.cli.ADAMMain \
  "$@"
