Merge a3f8f7e into 32dc0d4

.gitignore

@@ -22,12 +22,12 @@ parquettest.sh
 .idea/
 workfiles/
 chr20/
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/lib/
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/main/
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/test/
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/test.js
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/pileup.js
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/pileup.js.map
-mango-cli/src/main/webapp/resources/node_modules/pileup/dist/node_modules/
-mango-cli/src/main/webapp/resources/node_modules/pileup/node_modules/
-chr20/
+mango-play-*
+mango-play/public/resources/node_modules/pileup/dist/lib/
+mango-play/public/resources/node_modules/pileup/dist/main/
+mango-play/public/resources/node_modules/pileup/dist/test/
+mango-play/public/resources/node_modules/pileup/dist/test.js
+mango-play/public/resources/node_modules/pileup/dist/pileup.js
+mango-play/public/resources/node_modules/pileup/dist/pileup.js.map
+mango-play/public/resources/node_modules/pileup/dist/node_modules/
+mango-play/public/resources/node_modules/pileup/node_modules/

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "mango-cli/src/main/webapp/resources/pileup.js"]
-	path = mango-cli/src/main/webapp/resources/pileup.js
+[submodule "mango-play/public/resources/pileup.js"]
+	path = mango-play/public/resources/pileup.js
 	url = https://github.com/akmorrow13/pileup.js.git

README.md

@@ -1,4 +1,4 @@
-#mango
+# mango
 
 A scalable genome browser built on top of the [ADAM](https://github.com/bigdatagenomics/adam) genomics processing engine. Apache 2 licensed.
 
@@ -30,7 +30,9 @@ mango is packaged via [appassembler](http://mojo.codehaus.org/appassembler/appas
 
 Running an example script:
 ```
-From the main folder of mango, run ./example-files/run-example.sh to see a demonstration of chromosome 17, region 7500000-7515000.
+From the main folder of mango, run ./scripts/run-example.sh to see a demonstration of chromosome 17, region 7500000-7515000.
+```
+**Note:** In local mode, relative paths are referenced from the mango-play submodule. To reference your own files, put in the absolute path.
 ```
 For help launching the script, run `bin/mango-submit -h`
 ````

bin/compute-mango-classpath.sh

@@ -28,8 +28,8 @@ REPO="$SCRIPT_DIR/repo"
 
 # Fallback to source repo
 if [ ! -f $MANGO_CMD ]; then
-MANGO_CMD="$SCRIPT_DIR/mango-cli/target/appassembler/bin/mango"
-REPO="$SCRIPT_DIR/mango-cli/target/appassembler/repo"
+MANGO_CMD="$SCRIPT_DIR/mango-play/target/appassembler/bin/mango"
+REPO="$SCRIPT_DIR/mango-play/target/appassembler/repo"
 fi
 
 if [ ! -f "$MANGO_CMD" ]; then

bin/compute-spark-jars.sh

@@ -0,0 +1,64 @@
+#!/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.
+#
+
+set -e
+if [ -z "${SPARK_HOME}" ]; then
+  export SPARK_HOME="$(cd "`dirname "$0"`"/..; pwd)"
+fi
+
+. "${SPARK_HOME}"/bin/load-spark-env.sh
+
+# Find the java binary
+if [ -n "${JAVA_HOME}" ]; then
+  RUNNER="${JAVA_HOME}/bin/java"
+else
+  if [ `command -v java` ]; then
+    RUNNER="java"
+  else
+    echo "JAVA_HOME is not set" >&2
+    exit 1
+  fi
+fi
+
+# Find assembly jar
+SPARK_ASSEMBLY_JAR=
+if [ -f "${SPARK_HOME}/RELEASE" ]; then
+  ASSEMBLY_DIR="${SPARK_HOME}/lib"
+else
+  ASSEMBLY_DIR="${SPARK_HOME}/assembly/target/scala-$SPARK_SCALA_VERSION"
+fi
+
+GREP_OPTIONS=
+num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^spark-assembly.*hadoop.*\.jar$" | wc -l)"
+if [ "$num_jars" -eq "0" -a -z "$SPARK_ASSEMBLY_JAR" -a "$SPARK_PREPEND_CLASSES" != "1" ]; then
+  echo "Failed to find Spark assembly in $ASSEMBLY_DIR." 1>&2
+  echo "You need to build Spark before running this program." 1>&2
+  exit 1
+fi
+if [ -d "$ASSEMBLY_DIR" ]; then
+  ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^spark-assembly.*hadoop.*\.jar$" || true)"
+  if [ "$num_jars" -gt "1" ]; then
+    echo "Found multiple Spark assembly jars in $ASSEMBLY_DIR:" 1>&2
+    echo "$ASSEMBLY_JARS" 1>&2
+    echo "Please remove all but one jar." 1>&2
+    exit 1
+  fi
+fi
+
+echo "${ASSEMBLY_DIR}/${ASSEMBLY_JARS}"

bin/mango-install.sh

@@ -0,0 +1,28 @@
+#!/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.
+#
+
+set -e
+
+SCRIPT_DIR="$(cd `dirname $0`/..; pwd)"
+
+# build mango-play distribution
+mvn -f $SCRIPT_DIR play2:dist -pl mango-play
+
+# unzip new dist directory
+unzip -o "$SCRIPT_DIR/mango-play/target/mango-play-0.0.1-SNAPSHOT-dist.zip" -d $SCRIPT_DIR

bin/mango-submit

@@ -74,13 +74,29 @@ if [ -z "$SPARK_SUBMIT" ]; then
 fi
 echo "Using SPARK_SUBMIT=$SPARK_SUBMIT"
 
-# submit the job to Spark
-"$SPARK_SUBMIT" \
-  --class org.bdgenomics.mango.cli.VizReads \
-  --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
-  --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
-  --conf spark.dynamicAllocation.executorIdleTimeout=10d \
-  --conf spark.driver.memory=5g \
-  $SPARK_ARGS \
-  $MANGO_CLI_JAR \
-  $MANGO_ARGS
+# exports
+export SPARK_ARGS=$SPARK_ARGS
+export MANGO_MAIN_JAR=$MANGO_CLI_JAR
+export MANGO_ARGS=$MANGO_ARGS
+
+# generate application key
+APP_KEY=$(openssl rand -base64 15)
+export APPLICATION_SECRET=$APP_KEY
+
+SCRIPT_DIR="$(cd `dirname $0`/..; pwd)"
+
+# get version of mango from maven. This will be used to fetch the
+# most recently installed mango-play distribution
+MANGO_VERSION=`echo -e 'setns x=http://maven.apache.org/POM/4.0.0\ncat /x:project/x:version/text()' | xmllint --shell $SCRIPT_DIR/pom.xml | grep -v /`
+
+classpath="$SCRIPT_DIR/mango-play-$MANGO_VERSION/lib/*"
+
+# Get list of provided jars for spark
+SPARK_JARS=$("$SCRIPT_DIR"/bin/compute-spark-jars.sh)
+
+# modify classpath to include spark and hadoop
+# spark must come second do to dependency conflicts
+classpath="$classpath:$SPARK_JARS"
+
+# this is copied from playframework's autogenerated start script
+exec java $* -cp "$classpath" play.core.server.NettyServer $scriptdir