Refactored the docker build script to only only include the gatk bundle in order to shrink the docker image size

.dockerignore

@@ -1,3 +1,4 @@
 # These are files that for whatever reason we don't want to include in our distribution docker images
 src/test/resources
 src/test/resources/*
+.git/*

.travis.yml

@@ -21,7 +21,7 @@ env:
   #gradle needs this
   - TERM=dumb
   #limit gradle jvm memory and disable daemon
-  - GRADLE_OPTS="-Xmx1024m -Dorg.gradle.daemon=false"
+  - GRADLE_OPTS="-Xmx2048m -Dorg.gradle.daemon=false"
   #google cloud stuff
   - CLOUDSDK_CORE_DISABLE_PROMPTS=1
   - GCLOUD_HOME=$HOME/gcloud/google-cloud-sdk/bin
@@ -57,7 +57,7 @@ cache:
 before_install:
 - REPORT_PATH=${TRAVIS_BRANCH}_${TRAVIS_JOB_NUMBER};
 - if [[ $TRAVIS_SECURE_ENV_VARS == true && $TRAVIS_EVENT_TYPE != cron ]]; then
-    echo "Test report will be written to  https://storage.googleapis.com${HELLBENDER_TEST_LOGS}${REPORT_PATH}/tests/test/index.html";
+    echo "Test report will be written to  https://storage.googleapis.com$HELLBENDER_TEST_LOGS$REPORT_PATH/tests/test/index.html";
   fi
 #setup google cloud and github authentication
 - if [ $TRAVIS_SECURE_ENV_VARS == true ]; then
@@ -134,18 +134,19 @@ script:
   elif [[ $TEST_DOCKER == true ]]; then
     echo "Building docker image and running appropriate tests..." ;
     if [ ${TRAVIS_PULL_REQUEST} != false ]; then
-      sudo bash build_docker.sh  -e FETCH_HEAD -s -u -d $PWD/temp_staging/ -t ${TRAVIS_PULL_REQUEST};
+      sudo bash build_docker.sh  -e FETCH_HEAD -s -u -t ${TRAVIS_PULL_REQUEST};
       DOCKER_TAG=FETCH_HEAD;
     else
       echo ${TRAVIS_COMMIT};
-      sudo bash build_docker.sh  -e ${TRAVIS_COMMIT} -s -u -d $PWD/temp_staging/;
+      sudo bash build_docker.sh  -e ${TRAVIS_COMMIT} -s -u;
       DOCKER_TAG=$TRAVIS_COMMIT;
     fi;
     sudo docker images;
     echo ${TEST_TYPE};
     sudo mkdir -p build/reports/;
     sudo chmod -R a+w build/reports/;
-    sudo docker run -v $(pwd)/src/test/resources:/testdata -v $(pwd)/build/reports/:/gatk/build/reports/ --rm -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh;
+    cp scripts/docker/dockertest.gradle .;
+    sudo docker run -v $(pwd):/gatkCloneMountPoint:cached -v $(pwd)/testJars:/jars:cached --rm -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh && sudo mkdir build/reports/tests/test && sudo cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test && sudo rm -r build/reports/tests/testOnPackagedReleaseJar;
   else
     ./gatk PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam;
     travis_wait 50 ./gradlew jacocoTestReport;

Dockerfile

@@ -1,27 +1,41 @@
 # Using OpenJDK 8
-FROM broadinstitute/gatk:gatkbase-1.2.3
-ARG DRELEASE
+FROM broadinstitute/gatk:gatkbase-2.0.0
 
-ADD . /gatk
+# Location of the unzipped gatk bundle files
+ARG ZIPPATH
+
+ADD $ZIPPATH /gatk
 
 WORKDIR /gatk
-RUN /gatk/gradlew clean compileTestJava sparkJar localJar condaEnvironmentDefinition -Drelease=$DRELEASE
+
+#Setup linked jars that may be needed for running gatk
+RUN ln -s $( find /gatk -name "gatk*local.jar" ) gatk.jar
+RUN ln -s $( find /gatk -name "gatk*local.jar" ) /root/gatk.jar
+RUN ln -s $( find /gatk -name "gatk*spark.jar" ) gatk-spark.jar
 
 WORKDIR /root
 
-# Make sure we can see a help message
-RUN ln -sFv /gatk/build/libs/gatk.jar
+ # Make sure we can see a help message
 RUN java -jar gatk.jar -h
+RUN mkdir /gatkCloneMountPoint
+RUN mkdir /jars
+RUN mkdir .gradle
 
-#Setup test data
 WORKDIR /gatk
-# Create link to where test data is expected
-RUN ln -s /testdata src/test/resources
 
 # Create a simple unit test runner
 ENV CI true
 RUN echo "source activate gatk" > /root/run_unit_tests.sh && \
-    echo "cd /gatk/ && ./gradlew jacocoTestReport" >> /root/run_unit_tests.sh
+    echo "export TEST_JAR=\$( find /jars -name \"gatk*test.jar\" )" >> /root/run_unit_tests.sh && \
+    echo "export TEST_DEPENDENCY_JAR=\$( find /jars -name \"gatk*testDependencies.jar\" )" >> /root/run_unit_tests.sh && \
+    echo "export GATK_JAR=$( find /gatk -name "gatk*local.jar" )" >> /root/run_unit_tests.sh && \
+    echo "cp -rp /gatkCloneMountPoint/src/main/java/* /gatk/srcdir" >> /root/run_unit_tests.sh && \
+    echo "export SOURCE_DIR=/gatk/srcdir" >> /root/run_unit_tests.sh && \
+    echo "export GRADLE_OPTS=\"-Xmx1024m -Dorg.gradle.daemon=false\"" /root/run_unit_tests.sh && \
+    echo "export CP_DIR=/gatk/testClasses" /root/run_unit_tests.sh && \
+    echo "ln -s /gatkCloneMountPoint/src/ /gatkCloneMountPoint/scripts/docker/src" >> /root/run_unit_tests.sh && \
+    echo "ln -s /gatkCloneMountPoint/build/ /gatkCloneMountPoint/scripts/docker/build" >> /root/run_unit_tests.sh && \
+    echo "cd /gatk/ && /gatkCloneMountPoint/gradlew -b /gatkCloneMountPoint/dockertest.gradle testOnPackagedReleaseJar jacocoTestReportOnPackagedReleaseJar -a -p /gatkCloneMountPoint" >> /root/run_unit_tests.sh
 
 WORKDIR /root
 RUN cp -r /root/run_unit_tests.sh /gatk
@@ -39,16 +53,15 @@ RUN mkdir $DOWNLOAD_DIR && \
     test "`md5sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS='  ' '{print $1}'` = $CONDA_MD5" && \
     bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \
     rm $DOWNLOAD_DIR/miniconda.sh
-ENV PATH $CONDA_PATH/envs/gatk/bin:$CONDA_PATH/bin:$PATH
-WORKDIR /gatk/build
-RUN conda env create -n gatk -f gatkcondaenv.yml && \
-    echo "source activate gatk" >> /gatk/gatkenv.rc
 WORKDIR /gatk
+ENV PATH $CONDA_PATH/envs/gatk/bin:$CONDA_PATH/bin:$PATH
+RUN conda env create -n gatk -f /gatk/gatkcondaenv.yml && \
+    echo "source activate gatk" >> /gatk/gatkenv.rc && \
+    conda clean -y -all && \
+    rm -rf /root/.cache/pip
 
 CMD ["bash", "--init-file", "/gatk/gatkenv.rc"]
 
 # End GATK Python environment
 
-WORKDIR /gatk
-
 ENV PATH /gatk:$PATH

README.md

@@ -393,7 +393,7 @@ echo "source <PATH_TO>/gatk-completion.sh" >> ~/.bashrc
     * Test report is in `build/reports/tests/test/index.html`.
     * What will happen depends on the value of the `TEST_TYPE` environment variable: 
        * unset or any other value         : run non-cloud unit and integration tests, this is the default
-       * `cloud`, `unit`, `integration`, `spark`   : run only the cloud, unit, integration, or Spark tests
+       * `cloud`, `unit`, `integration`, `spark`, `python`   : run only the cloud, unit, integration, python, or Spark tests
        * `all`                            : run the entire test suite
     * Cloud tests require being logged into `gcloud` and authenticated with a project that has access
       to the cloud test data.  They also require setting several certain environment variables.

build.gradle

@@ -174,19 +174,6 @@ configurations.all {
     all*.exclude group: 'junit', module: 'junit'
 }
 
-
-jacocoTestReport {
-    dependsOn test
-    group = "Reporting"
-    description = "Generate Jacoco coverage reports after running tests."
-    additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
-
-    reports {
-        xml.enabled = true
-        html.enabled = true
-    }
-}
-
 //NOTE: we ignore contracts for now
 compileJava {
   options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose']
@@ -379,7 +366,6 @@ version = (isRelease ? gitVersion() : gitVersion() + "-SNAPSHOT").replaceAll(".d
 logger.info("build for version:" + version)
 group = 'org.broadinstitute'
 
-
 tasks.withType(Jar) {
     manifest {
         attributes 'Implementation-Title': 'The Genome Analysis Toolkit (GATK)',
@@ -390,7 +376,33 @@ tasks.withType(Jar) {
     }
 }
 
-test {
+task wrapper(type: Wrapper) {
+    gradleVersion = '3.1'
+}
+
+tasks.withType(ShadowJar) {
+    from(project.sourceSets.main.output)
+    baseName = project.name + '-package'
+    mergeServiceFiles()
+    relocate 'com.google.common', 'org.broadinstitute.hellbender.relocated.com.google.common'
+    zip64 true
+    exclude 'log4j.properties' // from adam jar as it clashes with hellbender's log4j2.xml
+    exclude '**/*.SF' // these are Manifest signature files and
+    exclude '**/*.RSA' // keys which may accidentally be imported from other signed projects and then fail at runtime
+
+    // Suggested by the akka devs to make sure that we do not get the spark configuration error.
+    // http://doc.akka.io/docs/akka/snapshot/general/configuration.html#When_using_JarJar__OneJar__Assembly_or_any_jar-bundler
+    transform(com.github.jengelman.gradle.plugins.shadow.transformers.AppendingTransformer) {
+        resource = 'reference.conf'
+    }
+}
+
+//============================================================================================================================
+// WARNING
+//============================================================================================================================
+// This is duplicated code with the build script in scripts/docker/dockertest.gradle. If you alter the tests in any way
+// please make sure to alter this test method there as well.
+tasks.withType(Test) {
     outputs.upToDateWhen { false }  //tests will never be "up to date" so you can always rerun them
     String TEST_VERBOSITY = "$System.env.TEST_VERBOSITY"
 
@@ -401,7 +413,11 @@ test {
      * anything else             : run the non-cloud tests
      */
     String TEST_TYPE = "$System.env.TEST_TYPE"
-
+//============================================================================================================================
+// WARNING
+//============================================================================================================================
+// This is duplicated code with the build script in scripts/docker/dockertest.gradle. If you alter the tests in any way
+// please make sure to alter this test method there as well.
     useTestNG {
         if (TEST_TYPE == "cloud") {
             // run only the cloud tests
@@ -473,28 +489,11 @@ test {
             }
         }
     }
-}
-
-
-task wrapper(type: Wrapper) {
-    gradleVersion = '3.1'
-}
-
-tasks.withType(ShadowJar) {
-    from(project.sourceSets.main.output)
-    baseName = project.name + '-package'
-    mergeServiceFiles()
-    relocate 'com.google.common', 'org.broadinstitute.hellbender.relocated.com.google.common'
-    zip64 true
-    exclude 'log4j.properties' // from adam jar as it clashes with hellbender's log4j2.xml
-    exclude '**/*.SF' // these are Manifest signature files and
-    exclude '**/*.RSA' // keys which may accidentally be imported from other signed projects and then fail at runtime
-
-    // Suggested by the akka devs to make sure that we do not get the spark configuration error.
-    // http://doc.akka.io/docs/akka/snapshot/general/configuration.html#When_using_JarJar__OneJar__Assembly_or_any_jar-bundler
-    transform(com.github.jengelman.gradle.plugins.shadow.transformers.AppendingTransformer) {
-        resource = 'reference.conf'
-    }
+//============================================================================================================================
+// WARNING
+//============================================================================================================================
+// This is duplicated code with the build script in scripts/docker/dockertest.gradle. If you alter the tests in any way
+// please make sure to alter this test method there as well.
 }
 
 shadowJar {
@@ -524,7 +523,27 @@ task sparkJar(type: ShadowJar) {
     }
 }
 
-task bundle(type: Zip) {
+// A jar that only contains the test classes and resources (to be extracted for testing)
+task shadowTestClassJar(type: ShadowJar){
+    group = "Shadow"
+    from sourceSets.test.output
+    description = "Create a jar that packages the compiled test classes"
+    classifier = "test"
+}
+
+// A minimal jar that only contains the extra dependencies needed for running the tests
+task shadowTestJar(type: ShadowJar){
+    group = "Shadow"
+    description = " A minimal jar that only contains the extra dependencies needed for running the tests that arent packaged in the main shadow jar"
+    from {
+        (project.configurations.testRuntime - project.configurations.runtime ).collect {
+            it.isDirectory() ? it : it.getName().endsWith(".jar") ? zipTree(it) : it
+        }
+    }
+    classifier = "testDependencies"
+}
+
+task collectBundleIntoDir(type: Copy) {
     dependsOn shadowJar, sparkJar, 'condaEnvironmentDefinition', 'gatkTabComplete', 'gatkDoc'
 
     doFirst {
@@ -534,10 +553,6 @@ task bundle(type: Zip) {
         assert file("src/main/resources/org/broadinstitute/hellbender/utils/config/GATKConfig.properties").exists()
     }
 
-    baseName = project.name + "-" + project.version
-    destinationDir file("$buildDir")
-    archiveName baseName + ".zip"
-
     from(shadowJar.archivePath)
     from(sparkJar.archivePath)
     from("gatk")
@@ -552,13 +567,40 @@ task bundle(type: Zip) {
     from("$buildDir/$pythonPackageArchiveName")
     from("$buildDir/$gatkCondaYML")
     from("$buildDir/$gatkCondaIntelYML")
+    from("scripts/sv", { into("scripts/sv") })
+    from("scripts/cnv_wdl/", { into("scripts/cnv_wdl") })
+    from("scripts/mutect2_wdl/", { into("scripts/mutect2_wdl") })
+    into "$buildDir/bundle-files-collected"
+}
+
+task bundle(type: Zip) {
+    dependsOn collectBundleIntoDir
+
+    baseName = project.name + "-" + project.version
+    destinationDir file("$buildDir")
+    archiveName baseName + ".zip"
+
+    from("$buildDir/bundle-files-collected")
     into(baseName)
 
     doLast {
         logger.lifecycle("Created GATK distribution in ${destinationDir}/${archiveName}")
     }
 }
 
+jacocoTestReport {
+    dependsOn test
+
+    group = "Reporting"
+    description = "Generate Jacoco coverage reports after running tests."
+    additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
+
+    reports {
+        xml.enabled = true
+        html.enabled = true
+    }
+}
+
 task condaStandardEnvironmentDefinition(type: Copy) {
     from "scripts"
     into buildDir

build_docker.sh

@@ -42,7 +42,6 @@ Optional arguments:  \n \
 	exit 1
 fi
 
-
 # -z is like "not -n"
 if [ -z ${IS_NOT_LATEST} ] && [ -n "${IS_HASH}" ] && [ -n "${IS_PUSH}" ]; then
 	echo -e "\n##################"
@@ -113,8 +112,22 @@ if [ -n "${IS_PUSH}" ]; then
 else
     RELEASE=false
 fi
+./gradlew clean collectBundleIntoDir shadowTestClassJar shadowTestJar -Drelease=$RELEASE
+ZIPPATHGATK=$( find ./build -name "*bundle-files-collected" )
+mv ${ZIPPATHGATK} ./unzippedJar
+ZIPPATHPYTHON=$( find ./unzippedJar -name "gatkPython*.zip" )
+unzip -o -j ${ZIPPATHPYTHON} -d ./unzippedJar/scripts
+
+mkdir ${STAGING_ABSOLUTE_PATH:-.}/testJars
+mv $( find ./build/libs/ -name "gatk*test.jar" ) ${STAGING_ABSOLUTE_PATH:-.}/testJars
+mv $( find ./build/libs/ -name "gatk*testDependencies.jar" ) ${STAGING_ABSOLUTE_PATH:-.}/testJars
+
 echo "Building image to tag ${REPO_PRJ}:${GITHUB_TAG}..."
-docker build -t ${REPO_PRJ}:${GITHUB_TAG} --build-arg DRELEASE=$RELEASE .
+if [ -n "${IS_PUSH}" ]; then
+    docker build -t ${REPO_PRJ}:${GITHUB_TAG} --squash --build-arg ZIPPATH=./unzippedJar .
+else
+    docker build -t ${REPO_PRJ}:${GITHUB_TAG} --build-arg ZIPPATH=./unzippedJar .
+fi
 
 if [ -z "${IS_NOT_RUN_UNIT_TESTS}" ] ; then
 
@@ -128,9 +141,13 @@ if [ -z "${IS_NOT_RUN_UNIT_TESTS}" ] ; then
 	git lfs pull
     chmod -R a+w ${STAGING_ABSOLUTE_PATH}/src/test/resources
 
-	echo docker run ${REMOVE_CONTAINER_STRING} -v ${STAGING_ABSOLUTE_PATH}/src/test/resources:/testdata -t ${REPO_PRJ}:${GITHUB_TAG} bash /root/run_unit_tests.sh
-	docker run ${REMOVE_CONTAINER_STRING} -v ${STAGING_ABSOLUTE_PATH}/src/test/resources:/testdata -t ${REPO_PRJ}:${GITHUB_TAG} bash /root/run_unit_tests.sh
+    cp build.gradle build.gradle.backup
+    cp /scripts/docker/dockertest.gradle .
+
+	echo docker run ${REMOVE_CONTAINER_STRING} -v  ${STAGING_ABSOLUTE_PATH}:/gatkCloneMountPoint -v  ${STAGING_ABSOLUTE_PATH}/testJars:/jars -t ${REPO_PRJ}:${GITHUB_TAG} bash /root/run_unit_tests.sh
+    docker run ${REMOVE_CONTAINER_STRING} -v  ${STAGING_ABSOLUTE_PATH}:/gatkCloneMountPoint -v  ${STAGING_ABSOLUTE_PATH}/testJars:/jars -t ${REPO_PRJ}:${GITHUB_TAG} bash /root/run_unit_tests.sh
 	echo " Unit tests passed..."
+	mv build.gradle.backup build.gradle
 fi
 
 ## Push