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[ADAM-429] adam-submit now handles args correctly. #430

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Oct 23, 2014
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[ADAM-429] adam-submit now handles args correctly. #430

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16 changes: 14 additions & 2 deletions bin/adam-submit
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
# Figure out where ADAM is installed
ADAM_REPO="$(cd `dirname $0`/..; pwd)"

CLASSPATH=$("$ADAM_REPO"/bin/compute-adam-classpath.sh)
# Get list of required jars for ADAM
ADAM_JARS=$("$ADAM_REPO"/bin/compute-adam-jars.sh)

# Find the ADAM CLI jar
Expand All @@ -39,13 +39,24 @@ if [ "$num_versions" -gt "1" ]; then
fi
ADAM_CLI_JAR=$(ls "$ADAM_REPO"/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli/*/adam-cli-*.jar)

# Find spark-submit script
if [ -z "$SPARK_HOME" ]; then
echo "Attempting to use 'spark-submit' on default path; you might need to set SPARK_HOME"
SPARK_SUBMIT=spark-submit
else
SPARK_SUBMIT="$SPARK_HOME"/bin/spark-submit
fi

# Split args into Spark args and ADAM args
# NOTE: if Spark uses gatherSparkSubmitOpts in spark-submit, this is unnecessary
function usage() {
echo "adam-submit <spark-args> <adam-args>"
exit 0
}
source "$SPARK_HOME"/bin/utils.sh
SUBMIT_USAGE_FUNCTION=usage
gatherSparkSubmitOpts "$@"

# submit the job to Spark
"$SPARK_SUBMIT" \
--class org.bdgenomics.adam.cli.ADAMMain \
Expand All @@ -54,5 +65,6 @@ fi
--conf spark.kryoserializer.buffer.mb=4 \
--conf spark.kryo.referenceTracking=true \
--jars "$ADAM_JARS" \
"${SUBMISSION_OPTS[@]}" \
"$ADAM_CLI_JAR" \
"$@"
"${APPLICATION_OPTS[@]}"