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build.gradle
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build.gradle
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buildscript {
repositories {
mavenCentral()
jcenter() // for shadow plugin
}
dependencies {
classpath 'org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.4.0'
classpath 'com.github.jengelman.gradle.plugins:shadow:1.2.2'
classpath 'com.github.ben-manes:gradle-versions-plugin:0.11.3' //used for identifying dependencies that need updating
}
}
plugins {
id "de.undercouch.download" version "1.2"
}
import de.undercouch.gradle.tasks.download.Download
apply plugin: 'java'
apply plugin: 'idea'
apply plugin: 'application'
apply plugin: "jacoco"
apply plugin: 'com.github.kt3k.coveralls'
apply plugin: 'maven'
apply plugin: 'signing'
apply plugin: 'com.github.johnrengelman.shadow'
apply plugin: 'com.github.ben-manes.versions'
mainClassName = "org.broadinstitute.hellbender.Main"
task downloadGsaLibFile(type: Download) {
src 'http://cran.r-project.org/src/contrib/gsalib_2.1.tar.gz'
dest "src/main/resources/org/broadinstitute/hellbender/utils/R/gsalib.tar.gz"
overwrite false
}
repositories {
mavenCentral()
jcenter()
maven {
url "https://repository.cloudera.com/artifactory/cloudera-repos/" // spark-dataflow
}
}
jacocoTestReport {
dependsOn test
group = "Reporting"
description = "Generate Jacoco coverage reports after running tests."
additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
reports {
xml.enabled = true // coveralls plugin depends on xml format report
html.enabled = true
}
}
jacoco {
toolVersion = "0.7.1.201405082137"
}
//NOTE: we ignore contracts for now
compileJava {
options.compilerArgs = ['-proc:none', '-Xlint:all','-Werror']
}
compileTestJava {
options.compilerArgs = ['-proc:none', '-Xlint:all','-Werror']
}
installApp.dependsOn downloadGsaLibFile
build.dependsOn installApp
check.dependsOn installApp
dependencies {
compile files("${System.properties['java.home']}/../lib/tools.jar")
compile 'com.github.samtools:htsjdk:1.137'
compile ('com.google.cloud.genomics:google-genomics-dataflow:v1beta2-0.14') {
// an upstream dependency includes guava-jdk5, but we want the newer version instead.
exclude module: 'guava-jdk5'
}
compile ('com.google.cloud.genomics:gatk-tools-java:1.1') {
exclude module: 'guava-jdk5'
}
compile 'org.apache.logging.log4j:log4j-api:2.3'
compile 'org.apache.logging.log4j:log4j-core:2.3'
compile 'org.apache.commons:commons-lang3:3.4'
compile 'org.apache.commons:commons-math3:3.5'
compile 'org.apache.commons:commons-collections4:4.0'
compile 'org.apache.commons:commons-vfs2:2.0'
compile 'commons-io:commons-io:2.4'
compile 'org.reflections:reflections:0.9.10'
compile 'net.sf.jopt-simple:jopt-simple:4.9'
compile 'com.google.cloud.dataflow:google-cloud-dataflow-java-sdk-all:0.4.150727'
compile ('com.google.apis:google-api-services-genomics:v1beta2-rev56-1.20.0') {
exclude module: 'guava-jdk5'
}
compile ('com.google.cloud.genomics:google-genomics-utils:v1beta2-0.30') {
exclude module: 'guava-jdk5'
}
compile 'com.google.guava:guava:18.0'
compile 'com.google.appengine.tools:appengine-gcs-client:0.4.4'
compile 'org.jgrapht:jgrapht-core:0.9.1'
compile 'org.testng:testng:6.9.6' //compile instead of testCompile because it is needed for test infrastructure that needs to be packaged
compile 'com.cloudera.dataflow.spark:spark-dataflow:0.3.0'
compile('org.seqdoop:hadoop-bam:7.1.0') {
exclude group: 'org.apache.hadoop'
exclude module: 'htsjdk'
}
compile('org.apache.hadoop:hadoop-client:2.7.1')
//needed for DataflowAssert
testCompile 'org.hamcrest:hamcrest-all:1.3'
testCompile 'junit:junit:4.12'
testCompile 'org.apache.hadoop:hadoop-minicluster:2.7.1'
testCompile "org.mockito:mockito-core:1.10.19"
testCompile('org.apache.spark:spark-core_2.10:1.4.1') {
// JUL is used by Google Dataflow as the backend logger, so exclude jul-to-slf4j to avoid a loop
exclude module: 'jul-to-slf4j'
exclude module: 'javax.servlet'
exclude module: 'servlet-api'
}
}
sourceCompatibility = 1.8
targetCompatibility = 1.8
def String deriveVersion(){
def stdout = new ByteArrayOutputStream()
try {
logger.info("path is $System.env.PATH")
exec {
commandLine "git", "describe", "--always"
standardOutput = stdout;
ignoreExitValue = true
}
} catch (GradleException e) {
logger.error("Couldn't determine version. " + e.getMessage())
}
return stdout.size() > 0 ? stdout.toString().trim() : "version-unknown"
}
final SNAPSHOT = "-SNAPSHOT"
version = deriveVersion() + SNAPSHOT //all builds are snapshot builds until we decide that there is something we want to keep
boolean isRelease = ! version.endsWith(SNAPSHOT)
logger.info("build for version:" + version)
group = 'org.broadinstitute'
jar {
manifest {
attributes 'Implementation-Title': 'Hellbender-tools',
'Implementation-Version': version,
'Main-Class': 'org.broadinstitute.hellbender.Main'
}
}
task testAll(type: Test){
useTestNG{}
// ensure dataflowRunner is passed to the test VM if specified on the command line
systemProperty "dataflowRunner", System.getProperty("dataflowRunner")
// increase max buffer size for Spark serialization
systemProperty "spark.kryoserializer.buffer.max", "256m"
// set heap size for the test JVM(s)
minHeapSize = "1G"
maxHeapSize = "2G"
// show standard out and standard error of the test JVM(s) on the console
testLogging.showStandardStreams = true
beforeTest { descriptor ->
logger.lifecycle("Running Test: " + descriptor)
}
// listen to standard out and standard error of the test JVM(s)
onOutput { descriptor, event ->
logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
}
}
test {
String CI = "$System.env.CI"
useTestNG{
if ( "$System.env.CLOUD" =="true"){
includeGroups 'cloud', 'bucket'
} else {
excludeGroups 'cloud', 'bucket'
}
}
// ensure dataflowRunner is passed to the test VM if specified on the command line
systemProperty "dataflowRunner", System.getProperty("dataflowRunner")
// increase max buffer size for Spark serialization
systemProperty "spark.kryoserializer.buffer.max", "256m"
// set heap size for the test JVM(s)
minHeapSize = "1G"
maxHeapSize = "2G"
if (CI == "true") {
int count = 0
// listen to events in the test execution lifecycle
testLogging {
events "skipped", "failed"
exceptionFormat = "full"
}
beforeTest { descriptor ->
count++
if( count % 10000 == 0) {
logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
}
}
} else {
// show standard out and standard error of the test JVM(s) on the console
testLogging.showStandardStreams = true
beforeTest { descriptor ->
logger.lifecycle("Running Test: " + descriptor)
}
// listen to standard out and standard error of the test JVM(s)
onOutput { descriptor, event ->
logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
}
}
}
task wrapper(type: Wrapper) {
gradleVersion = '2.2.1'
}
task fatJar(type: Jar) {
manifest {
attributes 'Implementation-Title': 'Hellbender',
'Implementation-Version': version,
'Main-Class': 'org.broadinstitute.hellbender.Main'
}
baseName = project.name + '-all'
from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
with jar
}
shadowJar {
manifest {
attributes 'Implementation-Title': 'Hellbender',
'Implementation-Version': version,
'Main-Class': 'org.broadinstitute.hellbender.Main'
}
baseName = project.name + '-all'
classifier = 'spark'
mergeServiceFiles()
relocate 'com.google.common', 'org.broadinstitute.hellbender.relocated.com.google.common'
zip64 true
dependencies {
// exclude Hadoop dependencies, since they are provided when running with Spark
exclude(dependency('org.apache.hadoop:.*:.*'))
exclude(dependency('org.xerial.snappy:snappy-java:.*'))
}
}
task javadocJar(type: Jar, dependsOn: javadoc) {
classifier = 'javadoc'
from 'build/docs/javadoc'
}
task sourcesJar(type: Jar) {
from sourceSets.main.allSource
classifier = 'sources'
}
// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
if (JavaVersion.current().isJava8Compatible()) {
tasks.withType(Javadoc) {
options.addStringOption('Xdoclint:none', '-quiet')
}
}
/**
*This specifies what artifacts will be built and uploaded when performing a maven upload.
*/
artifacts {
archives jar
archives javadocJar
archives sourcesJar
}
/**
* Sign non-snapshot releases with our secret key. This should never need to be invoked directly.
*/
signing {
required { isRelease && gradle.taskGraph.hasTask("uploadArchives") }
sign configurations.archives
}
/**
* Upload a release to sonatype. You must be an authorized uploader and have your sonatype
* username and password information in your gradle properties file. See the readme for more info.
*
* For releasing to your local maven repo, use gradle install
*/
uploadArchives {
if(project.hasProperty('sonatypeUsername') && project.hasProperty('sonatypePassword')){
repositories {
mavenDeployer {
beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }
repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
authentication(userName: sonatypeUsername, password: sonatypePassword)
}
snapshotRepository(url: "https://oss.sonatype.org/content/repositories/snapshots") {
authentication(userName: sonatypeUsername, password: sonatypePassword)
}
pom.project {
name 'Hellbender'
packaging 'jar'
description 'Development on GATK4'
url 'http://github.com/broadinstitute/hellbender'
scm {
url 'scm:[email protected]:broadinstitute/hellbender.git'
connection 'scm:[email protected]:broadinstitute/hellbender.git'
developerConnection 'scm:[email protected]:broadinstitute/hellbender.git'
}
licenses {
license {
name 'BSD 3-Clause'
url 'https://github.com/broadinstitute/hellbender/blob/master/LICENSE.TXT'
distribution 'repo'
}
}
}
}
}
} else {
doFirst({
logger.error( 'Users are not generally supposed to upload archives. ' +
'To upload archives you must specify certain information in your gradle.properties. See the README' +
' for more information.' )
throw new Exception("Missing sonatype username or password, please see the README for properties that must be specified for uploading an archive.")}
)
}
}