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build.gradle
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build.gradle
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// this file copied and modified from the GATK repository: https://github.com/broadinstitute/gatk
//
//Note: this section 'buildscript` is only for the dependencies of the buildscript itself.
// See the second 'repositories' section below for the actual dependencies of GATK itself
buildscript {
repositories {
mavenCentral()
jcenter() // for shadow plugin
}
}
plugins {
id "java" // set up default java compile and test tasks
id "application" // provides installDist
id "com.github.johnrengelman.shadow" version "2.0.4" //used to build the shadow and sparkJars
id 'com.palantir.git-version' version '0.5.1' //version helper
}
import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
import javax.tools.ToolProvider
apply plugin: 'java'
repositories {
mavenCentral()
jcenter()
maven {
url "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot/" //for htsjdk snapshots
}
mavenLocal()
}
//Note: the test suite must use the same defaults. If you change system properties in this list you must also update the one in the test task
applicationDefaultJvmArgs = ["-Dsamjdk.use_async_io_read_samtools=false","-Dsamjdk.use_async_io_write_samtools=true", "-Dsamjdk.use_async_io_write_tribble=false", "-Dsamjdk.compression_level=2"]
mainClassName = "org.broadinstitute.quartetibdanalysis.Main"
final requiredJavaVersion = "8"
final htsjdkVersion = System.getProperty('htsjdk.version','2.18.2')
final picardVersion = System.getProperty('picard.version','2.18.25')
final barclayVersion = System.getProperty('barclay.version','2.1.0')
final gatkVersion = System.getProperty('gatk.version','4.1.1.0')
final testNGVersion = '6.11'
// Using the shaded version to avoid conflicts between its protobuf dependency
// and that of Hadoop/Spark (either the one we reference explicitly, or the one
// provided by dataproc).
final googleCloudNioDependency = 'com.google.cloud:google-cloud-nio:0.81.0-alpha:shaded'
final docBuildDir = "$buildDir/docs"
logger.info(docBuildDir)
configurations.all {
resolutionStrategy {
// the snapshot folder contains a dev version of guava, we don't want to use that.
force 'com.google.guava:guava:18.0'
// force the htsjdk version so we don't get a different one transitively
force 'com.github.samtools:htsjdk:' + htsjdkVersion
// later versions explode Hadoop
force 'com.google.protobuf:protobuf-java:3.0.0-beta-1'
// force testng dependency so we don't pick up a different version via GenomicsDB
//force 'org.testng:testng:' + testNGVersion
force 'org.broadinstitute:barclay:' + barclayVersion
// make sure we don't pick up an incorrect version of the GATK variant of the google-nio library
// via Picard, etc.
force googleCloudNioDependency
}
all*.exclude group: 'org.slf4j', module: 'slf4j-jdk14' //exclude this to prevent slf4j complaining about to many slf4j bindings
all*.exclude group: 'com.google.guava', module: 'guava-jdk5'
all*.exclude group: 'junit', module: 'junit'
}
tasks.withType(JavaCompile) {
options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose']
}
sourceSets {
testUtils
}
// Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
// test execution, and gatkDoc generation, but we don't want them as part of the runtime
// classpath and we don't want to redistribute them in the uber jar.
//final javadocJDKFiles = files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())
configurations {
testUtilsCompile.extendsFrom compile
testUtilsRuntime.extendsFrom runtime
testCompile.extendsFrom testUtilsCompile
testRuntime.extendsFrom testUtilsRuntime
externalSourceConfiguration {
// External sources we need for doc and tab completion generation tasks (i.e., Picard sources)
transitive false
}
}
dependencies {
compile files('lib/SVToolkit.jar')
compile 'org.broadinstitute:gatk:' + gatkVersion
// javadoc utilities; compile/test only to prevent redistribution of sdk jars
//compileOnly(javadocJDKFiles)
//testCompile(javadocJDKFiles)
compile 'org.broadinstitute:barclay:' + barclayVersion
compile 'com.github.broadinstitute:picard:' + picardVersion
externalSourceConfiguration 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
compile 'com.opencsv:opencsv:3.4'
compile 'com.google.guava:guava:18.0'
compile 'com.github.samtools:htsjdk:'+ htsjdkVersion
compile googleCloudNioDependency
compile "gov.nist.math.jama:gov.nist.math.jama:1.1.1"
// this comes built-in when running on Google Dataproc, but the library
// allows us to read from GCS also when testing locally (or on non-Dataproc clusters,
// should we want to)
compile 'com.google.cloud.bigdataoss:gcs-connector:1.6.3-hadoop2'
compile 'org.apache.logging.log4j:log4j-api:2.3'
compile 'org.apache.logging.log4j:log4j-core:2.3'
// include the apache commons-logging bridge that matches the log4j version we use so
// messages that originate with dependencies that use commons-logging (such as jexl)
// are routed to log4j
compile 'org.apache.logging.log4j:log4j-jcl:2.3'
compile 'org.apache.commons:commons-lang3:3.5'
compile 'org.apache.commons:commons-math3:3.5'
compile 'org.apache.commons:commons-collections4:4.1'
compile 'org.apache.commons:commons-vfs2:2.0'
compile 'commons-io:commons-io:2.5'
compile 'org.reflections:reflections:0.9.10'
compile 'it.unimi.dsi:fastutil:7.0.6'
compile 'org.broadinstitute:hdf5-java-bindings:1.1.0-hdf5_2.11.0'
compile 'org.broadinstitute:gatk-native-bindings:1.0.0'
compile 'org.ojalgo:ojalgo:44.0.0'
compile ('org.ojalgo:ojalgo-commons-math3:1.0.0') {
exclude group: 'org.apache.commons'
}
// Required for SV Discovery machine learning
compile group: 'biz.k11i', name: 'xgboost-predictor', version: '0.3.0'
testUtilsCompile sourceSets.main.output
testUtilsCompile 'org.testng:testng:' + testNGVersion
testCompile sourceSets.testUtils.output
testUtilsCompile 'org.testng:testng:' + testNGVersion
testCompile "org.mockito:mockito-core:2.10.0"
testCompile "com.google.jimfs:jimfs:1.1"
}
//add gatk launcher script to the jar as a resource
processResources {
from("quartetibdanalysis")
}
sourceCompatibility = 1.8
targetCompatibility = 1.8
def createSymlinks(archivePath, symlinkLocation) {
exec {
commandLine 'ln', '-fs', archivePath, symlinkLocation
ignoreExitValue = false
}
}
// Suffix is what will be added to the symlink
def createGatkSymlinks(destinationDir, archivePath, suffix, baseJarName, secondaryBaseJarName) {
def finalSuffix = (suffix == "") ? "" : ("-" + suffix)
def symlinkLocation = destinationDir.toString() + "/" + baseJarName + finalSuffix + ".jar"
def symlinkLocation2 = destinationDir.toString() + "/" + secondaryBaseJarName + finalSuffix + ".jar"
createSymlinks(archivePath.getAbsolutePath(), symlinkLocation)
createSymlinks(archivePath.getAbsolutePath(), symlinkLocation2)
}
final isRelease = Boolean.getBoolean("release")
version = (isRelease ? gitVersion() : gitVersion() + "-SNAPSHOT").replaceAll(".dirty", "")
logger.info("build for version:" + version)
group = 'org.broadinstitute'
tasks.withType(Jar) {
manifest {
attributes 'Implementation-Title': 'Quartet IBD Analysis tools',
'Implementation-Version': version,
'Main-Class': project.mainClassName,
'GATK-Version': gatkVersion,
'Picard-Version': picardVersion,
'htsjdk-Version': htsjdkVersion
}
}
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'
}
}
apply from: "testsettings.gradle"
shadowJar {
configurations = [project.configurations.runtime]
classifier = 'local'
mergeServiceFiles('reference.conf')
doLast {
// Create a symlink to the newly created jar. The name will be gatk.jar and
// it will be at the same level as the newly created jar. (overwriting symlink, if it exists)
// Please note that this will cause failures in Windows, which does not support symlinks.
createGatkSymlinks(destinationDir.toString(), archivePath, "", baseJarName, secondaryBaseJarName)
}
}
task localJar{ dependsOn shadowJar }
// 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 javadocJar(type: Jar, dependsOn: javadoc) {
classifier = 'javadoc'
from "$docBuildDir/javadoc"
}
task sourcesJar(type: Jar) {
from sourceSets.main.allSource
classifier = 'sources'
}
task testUtilsJar(type: Jar){
baseName = "$project.name-test-utils"
from sourceSets.testUtils.output
}
tasks.withType(Javadoc) {
// do this for all javadoc tasks, including gatkDoc
options.addStringOption('Xdoclint:none')
}
javadoc {
// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
// We only want to do this for the javadoc task, not gatkDoc
options.addStringOption('Xdoclint:none', '-quiet')
source = sourceSets.main.allJava + files(configurations.externalSourceConfiguration.collect { zipTree(it) })
include '**/*.java'
}
task testUtilsJavadoc(type: Javadoc) {
// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
// We only want to do this for the javadoc task, not gatkDoc
options.addStringOption('Xdoclint:none', '-quiet')
source = sourceSets.testUtils.allJava
classpath = sourceSets.testUtils.runtimeClasspath
destinationDir = file("$docBuildDir/testUtilsJavadoc")
include '**/*.java'
}
task testUtilsJavadocJar(type: Jar, dependsOn: testUtilsJavadoc){
baseName = "$project.name-test-utils"
classifier = 'javadoc'
from "$docBuildDir/testUtilsJavadoc"
}
task testUtilsSourcesJar(type: Jar){
baseName = "$project.name-test-utils"
classifier = 'sources'
from sourceSets.testUtils.allSource
}
defaultTasks 'bundle'