Make picardcloud accessible in docker image (broadinstitute#1153)

* Added build script to build and push docker images

Author: tlangs

Dockerfile

@@ -1,6 +1,9 @@
 FROM broadinstitute/java-baseimage
 MAINTAINER Broad Institute DSDE <[email protected]>
 
+ARG build_command=shadowJar
+ARG jar_name=picard.jar
+
 # Install ant, git for building
 RUN apt-get update && \
     apt-get --no-install-recommends install -y --force-yes \
@@ -14,8 +17,8 @@ COPY / /usr/picard/
 WORKDIR /usr/picard
 
 # Build the distribution jar, clean up everything else
-RUN ./gradlew shadowJar && \
-    mv build/libs/picard.jar picard.jar && \
+RUN ./gradlew ${build_command} && \
+    mv build/libs/${jar_name} picard.jar && \
     mv src/main/resources/picard/docker_helper.sh docker_helper.sh && \
     ./gradlew clean && \
     rm -rf src && \

build_push_docker.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+# This script is used to build and deploy docker images for Picard
+
+if [[ "$1" == "" ]]
+then
+    echo "Usage: build_push_docker.sh <git-tag>"
+    exit 1
+fi
+
+declare -r TAG=${1}
+
+declare -r PICARD_TAG=broadinstitute/picard:${TAG}
+declare -r PICARD_CLOUD_TAG=us.gcr.io/broad-gotc-prod/picard-cloud:${TAG}
+
+echo "Will build and push the following docker images:"
+echo ${PICARD_TAG}
+echo ${PICARD_CLOUD_TAG}
+
+read -p "Is this really what you want to do? " -n 1 -r
+echo    # (optional) move to a new line
+if [[ $REPLY =~ ^[Yy]$ ]]
+then
+    docker build -t ${PICARD_TAG} --build-arg build_command=shadowJar --build-arg jar_name=picard.jar .
+    docker build -t ${PICARD_CLOUD_TAG} --build-arg build_command=cloudJar --build-arg jar_name=picardcloud.jar .
+
+    docker push ${PICARD_TAG}
+    gcloud docker -- push ${PICARD_CLOUD_TAG}
+fi

src/main/resources/picard/docker_helper.sh

@@ -24,4 +24,4 @@ done
 shift $(expr $OPTIND - 1)
 TOOL_WITH_ARGS=$@
 
-java ${JVM_ARGS} -jar /usr/picard/picard.jar ${TOOL_WITH_ARGS}
+java ${JVM_ARGS} -jar /usr/picard/picard*.jar ${TOOL_WITH_ARGS}