[ADAM-379] Fix the position of the jar path in the submit.

This accordingly with the spark documentation: http://spark.apache.org/docs/latest/submitting-applications.html.

That is, the jar must come after the `options` like --master and so on, but mainly --class. Otherwise, no `main` can be found in the JAR.

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala

@@ -30,18 +30,18 @@ object ADAMMain extends Logging {
   private val commandGroups =
     List(
       CommandGroup("ADAM ACTIONS", List(
-	CompareADAM,
-	FindReads,
-	CalculateDepth,
-	CountKmers,
-	PileupAggregator,
-	Transform,
-	/* TODO (nealsid): Reimplement in terms of new schema
+        CompareADAM,
+        FindReads,
+        CalculateDepth,
+        CountKmers,
+        PileupAggregator,
+        Transform,
+        /* TODO (nealsid): Reimplement in terms of new schema
 	  ComputeVariants
 	*/
-	PluginExecutor)),
+        PluginExecutor)),
       CommandGroup("CONVERSION OPERATIONS", List(
-	Bam2ADAM,
+        Bam2ADAM,
         Vcf2FlatGenotype,
         Vcf2ADAM,
         VcfAnnotation2ADAM,
@@ -51,7 +51,7 @@ object ADAMMain extends Logging {
         MpileupCommand,
         Features2ADAM)),
       CommandGroup("PRINT", List(
-	PrintADAM,
+        PrintADAM,
         FlagStat,
         VizReads,
         PrintTags,

adam-core/src/test/scala/org/bdgenomics/adam/util/SparkFunSuite.scala

@@ -36,13 +36,13 @@ trait SparkFunSuite extends FunSuite with BeforeAndAfter {
       val driverPort = s.getLocalPort
       s.close()
       val conf = new SparkConf(false)
-	.setAppName("adam: " + sparkName)
-	.setMaster("local[4]")
-	.set("spark.driver.port", driverPort.toString)
-	.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
-	.set("spark.kryo.registrator", "org.bdgenomics.adam.serialization.ADAMKryoRegistrator")
-	.set("spark.kryoserializer.buffer.mb", "4")
-	.set("spark.kryo.referenceTracking", "true")
+        .setAppName("adam: " + sparkName)
+        .setMaster("local[4]")
+        .set("spark.driver.port", driverPort.toString)
+        .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
+        .set("spark.kryo.registrator", "org.bdgenomics.adam.serialization.ADAMKryoRegistrator")
+        .set("spark.kryoserializer.buffer.mb", "4")
+        .set("spark.kryo.referenceTracking", "true")
       sc = new SparkContext(conf)
     }
   }

bin/adam-submit

@@ -48,8 +48,8 @@ fi
 
 # submit the job to Spark
 "$SPARK_SUBMIT" \
-  "$ADAM_CLI_JAR" \
   --class org.bdgenomics.adam.cli.ADAMMain \
   --properties-file "$ADAM_REPO"/bin/adam-spark-defaults.conf
   --jars "$ADAM_JARS" \
+  "$ADAM_CLI_JAR" \
   "$@"