From 9bd3f116c2a9cbca6d55288d77aff089b93c016e Mon Sep 17 00:00:00 2001
From: Uri Laserson <laserson@cloudera.com>
Date: Wed, 22 Oct 2014 18:06:51 -0700
Subject: [PATCH] [ADAM-429] adam-submit now handles args correctly.

Makes use of the `gatherSparkSubmitOpts` in Spark's `bin/utils.sh`. Fixes #429
---
 bin/adam-submit | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/bin/adam-submit b/bin/adam-submit
index 3712c95604..5be0e5620a 100755
--- a/bin/adam-submit
+++ b/bin/adam-submit
@@ -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
@@ -39,6 +39,7 @@ 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 "$SPARK_HOME" ]; then
   echo "Attempting to use 'spark-submit' on default path; you might need to set SPARK_HOME"
   SPARK_SUBMIT=spark-submit
@@ -46,6 +47,16 @@ else
   SPARK_SUBMIT="$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
 "$SPARK_SUBMIT" \
   --class org.bdgenomics.adam.cli.ADAMMain \
@@ -54,5 +65,6 @@ fi
   --conf spark.kryoserializer.buffer.mb=4 \
   --conf spark.kryo.referenceTracking=true \
   --jars "$ADAM_JARS" \
+  "${SUBMISSION_OPTS[@]}" \
   "$ADAM_CLI_JAR" \
-  "$@"
+  "${APPLICATION_OPTS[@]}"