diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
index 4679ee18f5..5fdcc956ed 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
@@ -24,8 +24,7 @@ import htsjdk.variant.variantcontext.writer.{
import htsjdk.variant.vcf.{ VCFHeader, VCFHeaderLine }
import java.io.OutputStream
import org.apache.hadoop.io.LongWritable
-import org.apache.hadoop.fs.{ FileSystem, Path }
-import org.apache.spark.Logging
+import org.apache.hadoop.fs.Path
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.converters.{
SupportedHeaderLines,
@@ -38,6 +37,7 @@ import org.bdgenomics.adam.models.{
}
import org.bdgenomics.adam.rdd.{ FileMerger, MultisampleGenomicRDD }
import org.bdgenomics.formats.avro.Sample
+import org.bdgenomics.utils.misc.Logging
import org.bdgenomics.utils.cli.SaveArgs
import org.seqdoop.hadoop_bam._
import scala.collection.JavaConversions._
diff --git a/pom.xml b/pom.xml
index 3c397489a3..67b21310f1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -28,7 +28,7 @@
7.6.0
1.7.21
0.9.0
- 0.2.7
+ 0.2.8-SNAPSHOT
2.5.0
1.1.1
diff --git a/scripts/jenkins-test b/scripts/jenkins-test
index 03f487a876..ec2bbf4ef5 100755
--- a/scripts/jenkins-test
+++ b/scripts/jenkins-test
@@ -38,6 +38,13 @@ then
exit 1
fi
+# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
+if [ ${SPARK_VERSION} == 2.0.0 ];
+then
+ echo "Rewriting POM.xml files for Scala 2.10."
+ ./scripts/move_to_spark_2.sh
+fi
+
# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
if [ ${SCALAVER} == 2.11 ];
then
diff --git a/scripts/move_to_spark_2.sh b/scripts/move_to_spark_2.sh
new file mode 100755
index 0000000000..5b829e49cc
--- /dev/null
+++ b/scripts/move_to_spark_2.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set +x
+
+find . -name "pom.xml" -exec sed -e "/utils-/ s/_2.10/-spark2_2.10/g" \
+ -e "/adam-/ s/_2.10/-spark2_2.10/g" \
+ -e "/spark.version/ s/1.6.1/2.0.0/g" \
+ -i .spark2.bak '{}' \;
diff --git a/scripts/release/release.sh b/scripts/release/release.sh
index 720d7b2c9d..631fd22953 100755
--- a/scripts/release/release.sh
+++ b/scripts/release/release.sh
@@ -38,7 +38,7 @@ mvn --batch-mode \
release:perform
if [ $? != 0 ]; then
- echo "Releasing Scala 2.10 version failed."
+ echo "Releasing Spark 1, Scala 2.10 version failed."
exit 1
fi
@@ -50,7 +50,7 @@ zip -r adam-${release}.zip adam-${release}.jar adam-${release}.pom
# do scala 2.11 release
git checkout -b maint_2.11-${release} ${branch}
./scripts/move_to_scala_2.11.sh
-git commit -a -m "Modifying pom.xml files for 2.11 release."
+git commit -a -m "Modifying pom.xml files for Spark 1, Scala 2.11 release."
mvn --batch-mode \
-P distribution \
-Dresume=false \
@@ -63,7 +63,47 @@ mvn --batch-mode \
release:perform
if [ $? != 0 ]; then
- echo "Releasing Scala 2.11 version failed."
+ echo "Releasing Spark 1, Scala 2.11 version failed."
+ exit 1
+fi
+
+# do spark 2, scala 2.11 release
+git checkout -b maint_spark2_2.11-${release} ${branch}
+./scripts/move_to_spark2.sh
+git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.11 release."
+mvn --batch-mode \
+ -P distribution \
+ -Dresume=false \
+ -Dtag=adam-parent-spark2_2.11-${release} \
+ -DreleaseVersion=${release} \
+ -DdevelopmentVersion=${devel} \
+ -DbranchName=adam-spark2_2.11-${release} \
+ release:clean \
+ release:prepare \
+ release:perform
+
+if [ $? != 0 ]; then
+ echo "Releasing Spark 2, Scala 2.11 version failed."
+ exit 1
+fi
+
+# do spark 2, scala 2.10 release
+git checkout -b maint_spark2_2.10-${release} ${branch}
+./scripts/move_to_scala_2.10.sh
+git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.10 release."
+mvn --batch-mode \
+ -P distribution \
+ -Dresume=false \
+ -Dtag=adam-parent-spark2_2.10-${release} \
+ -DreleaseVersion=${release} \
+ -DdevelopmentVersion=${devel} \
+ -DbranchName=adam-spark2_2.10-${release} \
+ release:clean \
+ release:prepare \
+ release:perform
+
+if [ $? != 0 ]; then
+ echo "Releasing Spark 2, Scala 2.10 version failed."
exit 1
fi