#!/usr/bin/env bash
#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The BDG licenses this file
# to you 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.
#

set -e

SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})

ADAM_CLI_JAR=$(${SOURCE_DIR}/find-adam-assembly.sh)

SPARKR=$(${SOURCE_DIR}/find-spark.sh sparkR)
echo "Using SPARKR=$SPARKR" 1>&2

# submit the job to Spark
"$SPARKR" \
    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
    --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
    --jars ${ADAM_CLI_JAR} \
    --driver-class-path ${ADAM_CLI_JAR} \
    "$@"

