variant-spark

#!/bin/bash

PWD=$(cd `dirname "$0"`; pwd)

if [[ -z "${VARIANT_SPARK_HOME}" ]]; then
	VARIANT_SPARK_HOME="${PWD}"
fi

if [[ -n "${VS_ECHO_CMDLINE}" ]]; then
	echo "$0" "$@"
fi

if [[ -d "${VARIANT_SPARK_HOME}/lib" ]]; then 
	VS_ASSEMBLY_DIR="${VARIANT_SPARK_HOME}/lib"
else
	VS_ASSEMBLY_DIR="${VARIANT_SPARK_HOME}/target"
fi 
	
VS_ASSEMBLY_JAR=$(echo ${VS_ASSEMBLY_DIR}/variant-spark_*-all.jar)

RUNNER="--spark"
declare -a SPARK_PARAMS 
spark_param_index=0
if [[ "$1" == "--spark"  || "$1" == "--emr" || "$1" == "--local" ]]; then
	RUNNER="$1"
	shift 1
	while [[ "$#" -gt 0 ]]; do
		arg="$1"
		shift 1
		if [[ "$arg" == "--" ]]; then
			break
		fi
		SPARK_PARAMS[spark_param_index]="$arg"
		((spark_param_index+=1))
	done
fi

if [[ -n "${VS_DEBUG}" ]]; then
	echo "Home: ${VARIANT_SPARK_HOME} "
	echo "Runner: ${RUNNER}"
	echo "Jar: ${VS_ASSEMBLY_JAR}"
fi

if [[ "${RUNNER}" == "--spark" ]]; then
	spark-submit --class au.csiro.variantspark.cli.VariantSparkApp \
 	--driver-class-path ${VARIANT_SPARK_HOME}/conf \
 	"${SPARK_PARAMS[@]}" \
 	${VS_ASSEMBLY_JAR} "$@"
elif [[ "${RUNNER}" == "--emr" ]]; then
	spark-submit --class au.csiro.variantspark.cli.VariantSparkApp \
 	"${SPARK_PARAMS[@]}" \
 	${VS_ASSEMBLY_JAR} "$@"
else
	SPARK_JARS="${SPARK_HOME}/jars/*"
	SPARK_CLASSPATH="${VARIANT_SPARK_HOME}/conf:${VS_ASSEMBLY_JAR}:${SPARK_JARS}:/usr/lib/hadoop/lib/*:/usr/lib/hadoop/.//*:/usr/lib/hadoop-hdfs/./:/usr/lib/hadoop-hdfs/lib/*:/usr/lib/hadoop-hdfs/.//*:/usr/lib/hadoop-yarn/lib/*:/usr/lib/hadoop-yarn/.//*:/usr/lib/hadoop-mapreduce/lib/*:/usr/lib/hadoop-mapreduce/.//*"
        echo "$SPARK_CLASSPATH"
	java -cp "${SPARK_CLASSPATH}" "${SPARK_PARAMS[@]}"  au.csiro.variantspark.cli.VariantSparkApp "$@"
fi