Update Dockerfile and build_push_docker.sh (#1921)

* This adjust for the lack of picard cloud jar and properly sets the picard version
so it's not listed as "snapshot"
* Update the docker build to use staged builds.
  This reduces the build size from about 1.7gb to about 650mb

Dockerfile

@@ -1,31 +1,37 @@
-FROM eclipse-temurin:17-jdk
-MAINTAINER Broad Institute DSDE <[email protected]>
+ARG BASE_DOCKER=eclipse-temurin:17-jdk
+ARG release=false
 
-ARG build_command=shadowJar
-ARG jar_name=picard.jar
+FROM ${BASE_DOCKER} as build
+LABEL stage=buildStage
 
-# Install ant, git for building
+# Install git for building
 RUN apt-get update && \
     apt-get --no-install-recommends install -y \
-        git \
-        r-base \
-        ant && \
-    apt-get clean autoclean && \
-    apt-get autoremove -y
+        git
 
 # Assumes Dockerfile lives in root of the git repo. Pull source files into container
 COPY / /usr/picard/
 WORKDIR /usr/picard
 
-# Build the distribution jar, clean up everything else
-RUN ./gradlew ${build_command} && \
-    mv build/libs/${jar_name} picard.jar && \
-    ./gradlew clean && \
-    rm -rf src && \
-    rm -rf gradle && \
-    rm -rf .git && \
-    rm gradlew && \
-    rm build.gradle
+# download gradle then build
+RUN ./gradlew -Drelease=${release} \
+   clean \
+   printVersion \
+   shadowJar
+
+FROM ${BASE_DOCKER} as final
+MAINTAINER Broad Institute DSDE <[email protected]>
+
+# Install R
+RUN apt-get update && \
+    apt-get --no-install-recommends install -y \
+        r-base &&\
+    apt-get clean autoclean && \
+    apt-get autoremove -y
+
+RUN mkdir /usr/picard/
+
+COPY --from=build /usr/picard/build/libs/picard.jar /usr/picard/
 
 RUN mkdir /usr/working
-WORKDIR /usr/working
+WORKDIR /usr/working

build_push_docker.sh

@@ -20,6 +20,6 @@ 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_CLOUD_TAG} --build-arg build_command=cloudJar --build-arg jar_name=picardcloud.jar .
+    docker build -t ${PICARD_CLOUD_TAG} --build-arg release=true .
     docker push ${PICARD_CLOUD_TAG}
 fi