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.project | ||
.manager | ||
.scala_dependencies | ||
.iml | ||
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# idea | ||
*.idea | ||
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#!/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. | ||
# | ||
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set -e | ||
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# Split args into Spark and GNOCCHI args | ||
DD=False # DD is "double dash" | ||
PRE_DD=() | ||
POST_DD=() | ||
for ARG in "$@"; do | ||
shift | ||
if [[ $ARG == "--" ]]; then | ||
DD=True | ||
POST_DD=( "$@" ) | ||
break | ||
fi | ||
PRE_DD+=("$ARG") | ||
done | ||
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if [[ $DD == True ]]; then | ||
SPARK_ARGS=("${PRE_DD[@]}") | ||
GNOCCHI_ARGS=("${POST_DD[@]}") | ||
else | ||
SPARK_ARGS=() | ||
GNOCCHI_ARGS=("${PRE_DD[@]}") | ||
fi | ||
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# Figure out where GNOCCHI is installed | ||
SCRIPT_DIR="$(cd `dirname $0`/..; pwd)" | ||
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# does the user have GNOCCHI_OPTS set? if yes, then warn | ||
if [[ -z $@ && -n "$GNOCCHI_OPTS" ]]; then | ||
echo "WARNING: Passing Spark arguments via GNOCCHI_OPTS was recently removed." | ||
echo "Run gnocchi-shell instead as gnocchi-shell <spark-args>" | ||
fi | ||
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# Find GNOCCHI cli assembly jar | ||
GNOCCHI_CLI_JAR= | ||
if [ -d "$SCRIPT_DIR/repo" ]; then | ||
ASSEMBLY_DIR="$SCRIPT_DIR/repo" | ||
else | ||
ASSEMBLY_DIR="$SCRIPT_DIR/gnocchi-assembly/target" | ||
fi | ||
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num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)" | ||
if [ "$num_jars" -eq "0" ]; then | ||
echo "Failed to find GNOCCHI assembly in $ASSEMBLY_DIR." 1>&2 | ||
echo "You need to build GNOCCHI before running this program." 1>&2 | ||
exit 1 | ||
fi | ||
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ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)" | ||
if [ "$num_jars" -gt "1" ]; then | ||
echo "Found multiple GNOCCHI cli assembly jars in $ASSEMBLY_DIR:" 1>&2 | ||
echo "$ASSEMBLY_JARS" 1>&2 | ||
echo "Please remove all but one jar." 1>&2 | ||
exit 1 | ||
fi | ||
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GNOCCHI_CLI_JAR="${ASSEMBLY_DIR}/${ASSEMBLY_JARS}" | ||
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if [ -z "$SPARK_HOME" ]; then | ||
SPARK_SHELL=$(which spark-shell || echo) | ||
else | ||
SPARK_SHELL="$SPARK_HOME"/bin/spark-shell | ||
fi | ||
if [ -z "$SPARK_SHELL" ]; then | ||
echo "SPARK_HOME not set and spark-shell not on PATH; Aborting." | ||
exit 1 | ||
fi | ||
echo "Using SPARK_SHELL=$SPARK_SHELL" | ||
echo "Welcome to" | ||
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ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" | ||
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cat "$ABSOLUTE_PATH/logo.txt" | ||
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# submit the job to Spark | ||
"$SPARK_SHELL" \ | ||
--conf spark.serializer=org.apache.spark.serializer.KryoSerializer \ | ||
--conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \ | ||
"${SPARK_ARGS[@]}" \ | ||
--jars ${GNOCCHI_CLI_JAR} \ | ||
"$@" |
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