build.gradle

//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 'maven'          // record code coverage during test execution
    id 'signing'
    id "jacoco"
    id "de.undercouch.download" version "2.1.0" //used for downloading GSA lib
    id "com.github.johnrengelman.shadow" version "1.2.3"    //used to build the shadow and sparkJars
    id "com.github.ben-manes.versions" version "0.12.0" //used for identifying dependencies that need updating
    id 'com.palantir.git-version' version '0.5.1' //version helper
}


import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
import de.undercouch.gradle.tasks.download.Download

import javax.tools.ToolProvider

mainClassName = "org.broadinstitute.hellbender.Main"

//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"]

//Delete the windows script - we never test on Windows so let's not pretend it works
startScripts {
    doLast {
        delete windowsScript
    }
}

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://broadinstitute.jfrog.io/broadinstitute/libs-snapshot/" //for htsjdk snapshots
    }

    mavenLocal()
}

final requiredJavaVersion = "8"
final htsjdkVersion = System.getProperty('htsjdk.version','2.16.1')
final picardVersion = System.getProperty('picard.version','2.18.13')
final barclayVersion = System.getProperty('barclay.version','2.1.0')
final sparkVersion = System.getProperty('spark.version', '2.2.0')
final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
final hadoopBamVersion = System.getProperty('hadoopBam.version','7.10.0')
final tensorflowVersion = System.getProperty('tensorflow.version','1.4.0')
final genomicsdbVersion = System.getProperty('genomicsdb.version','0.9.2-proto-3.0.0-beta-1+ab5fbe92900259')
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:0.62.0-alpha:shaded'

final baseJarName = 'gatk'
final secondaryBaseJarName = 'hellbender'
final docBuildDir = "$buildDir/docs"
final pythonPackageArchiveName = 'gatkPythonPackageArchive.zip'
final gatkCondaTemplate = "gatkcondaenv.yml.template"
final gatkCondaYML = "gatkcondaenv.yml"
final largeResourcesFolder = "src/main/resources/large"
final buildPrerequisitesMessage = "See https://github.com/broadinstitute/gatk#building for information on how to build GATK."

// Returns true if any files in the target folder are git-lfs stub files.
def checkForLFSStubFiles(targetFolder) {
    final lfsStubFileHeader = "version https://git-lfs.github.com/spec/v1"  // first line of a git-lfs stub file
    def readBytesFromFile = { largeFile, n ->
        final byte[] bytes = new byte[n]
        largeFile.withInputStream { stream -> stream.read(bytes, 0, bytes.length) }
        return bytes
    }
    def targetFiles = fileTree(dir: targetFolder)
    return targetFiles.any() { f ->
        final byte[] actualBytes = readBytesFromFile(f, lfsStubFileHeader.length());
        return new String(actualBytes, "UTF-8") == lfsStubFileHeader
    }
}

// if any of the large resources are lfs stub files, download them
def resolveLargeResourceStubFiles(largeResourcesFolder, buildPrerequisitesMessage) {
    def execGitLFSCommand = { gitLFSExecCommand ->
        println "Executing: $gitLFSExecCommand"
        try {
            def retCode = gitLFSExecCommand.execute().waitFor()
            if (retCode.intValue() != 0) {
                throw new GradleException("Execution of \"$gitLFSExecCommand\" failed with exit code: $retCode. " +
                        " git-lfs is required to build GATK but may not be installed. $buildPrerequisitesMessage");
            }
            return retCode
        } catch (IOException e) {
            throw new GradleException(
                    "An IOException occurred while attempting to execute the command $gitLFSExecCommand."
                    + " git-lfs is required to build GATK but may not be installed. $buildPrerequisitesMessage", e)
        }
    }

    // check for stub files, try to pull once if there are any, then check again
    if (checkForLFSStubFiles(largeResourcesFolder)) {
        final gitLFSPullLargeResources = "git lfs pull --include $largeResourcesFolder"
        execGitLFSCommand(gitLFSPullLargeResources)
        if (checkForLFSStubFiles(largeResourcesFolder)) {
            throw new GradleException("$largeResourcesFolder contains one or more git-lfs stub files."
                    + " The resource files in $largeResourcesFolder must be downloaded by running the git-lfs"
                    + " command \"$gitLFSPullLargeResources\". $buildPrerequisitesMessage")
        }
    }
}

// Ensure that we have the right JDK version, a clone of the git repository, and resolve any required git-lfs
// resource files that are needed to run the build but are still lfs stub files.
def ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequisitesMessage) {
    // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
    if (ToolProvider.getSystemToolClassLoader() == null) {
        throw new GradleException(
                "The ClassLoader obtained from the Java ToolProvider is null. "
                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
    }
    if (!file(".git").isDirectory()) {
        throw new GradleException("The GATK Github repository must be cloned using \"git clone\" to run the build. "
                + "$buildPrerequisitesMessage")
    }
    // Large runtime resource files must be present at build time to be compiled into the jar, so
    // try to resolve them to real files if any of them are stubs.
    resolveLargeResourceStubFiles(largeResourcesFolder, buildPrerequisitesMessage)
}

ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequisitesMessage)

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'
}

//NOTE: we ignore contracts for now
compileJava {
  options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose']
}
compileTestJava {
  options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose']
}


sourceSets {
    testUtils
}

// Dependency change for including MLLib
configurations {
    testUtilsCompile.extendsFrom compile
    testUtilsRuntime.extendsFrom runtime

    testCompile.extendsFrom testUtilsCompile
    testRuntime.extendsFrom testUtilsRuntime

    compile.exclude module: 'jul-to-slf4j'
    compile.exclude module: 'javax.servlet'
    compile.exclude module: 'servlet-api'
    compile.exclude group: 'com.esotericsoftware.kryo'

    externalSourceConfiguration {
        // External sources we need for doc and tab completion generation tasks (i.e., Picard sources)
        transitive false
    }

    sparkConfiguration {
        extendsFrom runtime
        // exclude Hadoop and Spark dependencies, since they are provided when running with Spark
        // (ref: http://unethicalblogger.com/2015/07/15/gradle-goodness-excluding-depends-from-shadow.html)
        exclude group: 'org.apache.hadoop'
        exclude module: 'spark-core_2.11'
        exclude group: 'org.slf4j'
        exclude module: 'jul-to-slf4j'
        exclude module: 'javax.servlet'
        exclude module: 'servlet-api'
        exclude group: 'com.esotericsoftware.kryo'
        exclude module: 'spark-mllib_2.11'
        exclude group: 'org.scala-lang'
        exclude module: 'kryo'
    }
}

// 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())

dependencies {
    // javadoc utilities; compile/test only to prevent redistribution of sdk jars
    compileOnly(javadocJDKFiles)
    testCompile(javadocJDKFiles)

    compile 'org.broadinstitute:barclay:' + barclayVersion
    // Library for configuration:
    compile 'org.aeonbits.owner:owner:1.0.9'

    compile 'com.github.broadinstitute:picard:' + picardVersion
    externalSourceConfiguration 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
    compile ('com.intel:genomicsdb:' + genomicsdbVersion)  {
        exclude module: 'log4j'
        exclude module: 'spark-core_2.10'
        exclude module: 'htsjdk'
        exclude module: 'protobuf-java'
    }
    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'
    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'
    }
    compile ('org.apache.spark:spark-mllib_2.11:' + sparkVersion) {
        // 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'
    }

    compile 'org.bdgenomics.bdg-formats:bdg-formats:0.5.0'
    compile('org.bdgenomics.adam:adam-core-spark2_2.11:0.20.0') {
        exclude group: 'org.slf4j'
        exclude group: 'org.apache.hadoop'
        exclude group: 'org.scala-lang'
        exclude module: 'kryo'
        exclude module: 'hadoop-bam'
    }

    compile 'org.jgrapht:jgrapht-core:0.9.1'

    compile('org.seqdoop:hadoop-bam:' + hadoopBamVersion) {
        exclude group: 'org.apache.hadoop'
        exclude module: 'htsjdk'
    }
    compile('org.apache.hadoop:hadoop-client:' + hadoopVersion) // should be a 'provided' dependency
    compile('com.github.jsr203hadoop:jsr203hadoop:1.0.3')

    compile('de.javakaffee:kryo-serializers:0.41') {
        exclude module: 'kryo' // use Spark's version
    }

    // Dependency change for including MLLib
    compile('org.objenesis:objenesis:1.2')
    testCompile('org.objenesis:objenesis:2.1')

    // Comment the next lines to disable native code proxies in Spark MLLib
    compile('com.github.fommil.netlib:netlib-native_ref-osx-x86_64:1.1:natives')
    compile('com.github.fommil.netlib:netlib-native_ref-linux-x86_64:1.1:natives')
    compile('com.github.fommil.netlib:netlib-native_system-linux-x86_64:1.1:natives')
    compile('com.github.fommil.netlib:netlib-native_system-osx-x86_64:1.1:natives')

    // Dependency change for including MLLib
    compile('com.esotericsoftware:kryo:3.0.3'){
        exclude group: 'com.esotericsoftware', module: 'reflectasm'
        exclude group: 'org.ow2.asm', module: 'asm'
    }

    // Dependency change for including MLLib
    compile('com.esotericsoftware:reflectasm:1.10.0:shaded')

    compile('com.intel.gkl:gkl:0.8.5') {
        exclude module: 'htsjdk'
    }

    compile 'org.broadinstitute:gatk-bwamem-jni:1.0.4'
    compile 'org.broadinstitute:gatk-fermilite-jni:1.2.0'

    // Required for COSMIC Funcotator data source:
    compile 'org.xerial:sqlite-jdbc:3.20.1'
    
    // 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
    testUtilsCompile 'org.apache.hadoop:hadoop-minicluster:' + hadoopVersion

    testCompile sourceSets.testUtils.output

    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("gatk")
}

processTestResources {
    //Don't waste time packaging unnecessary test data into the test resources:
    include "org/broadinstitute/hellbender/utils/config/*"
    //Required for IOUtils resource tests
    include "org/broadinstitute/hellbender/utils/io/*"
}

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': 'The Genome Analysis Toolkit (GATK)',
                'Implementation-Version': version,
                'Main-Class': project.mainClassName,
                'Picard-Version': picardVersion,
                'htsjdk-Version': htsjdkVersion
    }
}

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'
    }
}

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 }

task sparkJar(type: ShadowJar) {
    group = "Shadow"
    description = "Create a combined jar of project and runtime dependencies that excludes provided spark dependencies"
    configurations = [project.configurations.sparkConfiguration]
    classifier = 'spark'
    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, classifier, baseJarName, secondaryBaseJarName)
    }
}

// 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 {
        assert file("gatk").exists()
        assert file("README.md").exists()
        assert file("$docBuildDir/tabCompletion/gatk-completion.sh").exists()
        assert file("src/main/resources/org/broadinstitute/hellbender/utils/config/GATKConfig.properties").exists()
    }

    from(shadowJar.archivePath)
    from(sparkJar.archivePath)
    from("gatk")
    from("README.md")
    from("$docBuildDir/tabCompletion/gatk-completion.sh")
    from("$docBuildDir/gatkDoc", { into("gatkdoc") })

    from("src/main/resources/org/broadinstitute/hellbender/utils/config/GATKConfig.properties") {
        rename 'GATKConfig.properties', 'GATKConfig.EXAMPLE.properties'
    }

    from("$buildDir/$pythonPackageArchiveName")
    from("$buildDir/$gatkCondaYML")
    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
    include gatkCondaTemplate
    rename { file -> gatkCondaYML }
    expand(["condaEnvName":"gatk",
            "condaEnvDescription" : "Conda environment for GATK Python Tools"])
    doLast {
        logger.lifecycle("Created standard Conda environment yml file: $gatkCondaYML")
    }
}


// Create a GATK conda environment yml file from the conda enc template
// (used TensorFlow with Intel hardware acceleration).
task condaEnvironmentDefinition() {
    dependsOn 'pythonPackageArchive', 'condaStandardEnvironmentDefinition'
}

// Create the Python package archive file
task pythonPackageArchive(type: Zip) {
    inputs.dir "src/main/python/org/broadinstitute/hellbender/"
    outputs.file pythonPackageArchiveName
    doFirst {
        assert file("src/main/python/org/broadinstitute/hellbender/").exists()
    }

    destinationDir file("${buildDir}")
    archiveName pythonPackageArchiveName
    from("src/main/python/org/broadinstitute/hellbender/")
    into("/")

    doLast {
        logger.lifecycle("Created GATK Python package archive in ${destinationDir}/${archiveName}")
    }
}

// Creates a standard, local, GATK conda environment, for use by developers during iterative
// development. Assumes conda or miniconda is already installed.
//
// NOTE: This CREATES a local conda environment; but does not *activate* it. The environment must
// be activated manually in the shell from which GATK will be run.
//
task localDevCondaEnv(type: Exec) {
    dependsOn 'condaEnvironmentDefinition'
    inputs.file("$buildDir/$pythonPackageArchiveName")
    workingDir "$buildDir"
    commandLine "conda", "env", "update", "-f", gatkCondaYML
}

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
}

// Generate GATK Online Doc
task gatkDoc(type: Javadoc, dependsOn: classes) {
    final File gatkDocDir = new File("$docBuildDir/gatkdoc")
    doFirst {
        // make sure the output folder exists or we can create it
        if (!gatkDocDir.exists() && !gatkDocDir.mkdirs()) {
            throw new GradleException(String.format("Failure creating folder (%s) for GATK doc output in task (%s)",
                    gatkDocDir.getAbsolutePath(),
                    it.name));
        }
        copy {
            from('src/main/resources/org/broadinstitute/hellbender/utils/helpTemplates')
            include 'gatkDoc.css'
            into gatkDocDir
        }
    }
    // Include the Picard source jar, which contains various .R, .sh, .css, .html, .xml and .MF files and
    // other resources, but we only want the files that javadoc can handle, so just take the .java files.
    source = sourceSets.main.allJava + files(configurations.externalSourceConfiguration.collect { zipTree(it) })
    include '**/*.java'

    // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
    // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
    classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
    options.docletpath = classpath.asType(List)
    options.doclet = "org.broadinstitute.hellbender.utils.help.GATKHelpDoclet"

    outputs.dir(gatkDocDir)
    options.destinationDirectory(gatkDocDir)

    options.addStringOption("settings-dir", "src/main/resources/org/broadinstitute/hellbender/utils/helpTemplates");
    if (project.hasProperty('phpDoc')) {
        // use -PphpDoc to generate .php file extensions, otherwise rely on default of .html
        final String phpExtension = "php"
        options.addStringOption("output-file-extension", phpExtension)
        options.addStringOption("index-file-extension", phpExtension)
    }
    options.addStringOption("absolute-version", getVersion())
    options.addStringOption("build-timestamp", new Date().format("dd-mm-yyyy hh:mm:ss"))
}

// Generate GATK Bash Tab Completion File
task gatkTabComplete(type: Javadoc, dependsOn: classes) {
    final File tabCompletionDir = new File("$docBuildDir/tabCompletion")
    doFirst {
        // make sure the output folder exists or we can create it
        if (!tabCompletionDir.exists() && !tabCompletionDir.mkdirs()) {
            throw new GradleException(String.format("Failure creating folder (%s) for GATK tab completion output in task (%s)",
                    tabCompletionDir.getAbsolutePath(),
                    it.name));
        }
    }
    // Include the Picard source jar, which contains various .R, .sh, .css, .html, .xml and .MF files and
    // other resources, but we only want the files that javadoc can handle, so just take the .java files.
    source = sourceSets.main.allJava + files(configurations.externalSourceConfiguration.collect { zipTree(it) })
    include '**/*.java'

    // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
    // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives, and Picard.
    classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles

    options.docletpath = classpath.asType(List)
    options.doclet = "org.broadinstitute.barclay.help.BashTabCompletionDoclet"

    outputs.dir(tabCompletionDir)
    options.destinationDirectory(tabCompletionDir)

    // This is a hack to work around a gross Gradle bug:
    options.addStringOption('use-default-templates', '-use-default-templates')

    options.addStringOption("output-file-extension", "sh")
    options.addStringOption("index-file-extension", "sh")
    options.addStringOption("absolute-version", getVersion())
    options.addStringOption("build-timestamp", new Date().format("dd-mm-yyyy hh:mm:ss"))

    options.addStringOption("caller-script-name", "gatk")

    options.addStringOption("caller-pre-legal-args", "--help --list --dry-run --java-options")
    options.addStringOption("caller-pre-arg-val-types", "null null null String")
    options.addStringOption("caller-pre-mutex-args", "--help;list,dry-run,java-options --list;help,dry-run,java-options")
    options.addStringOption("caller-pre-alias-args", "--help;-h")
    options.addStringOption("caller-pre-arg-min-occurs", "0 0 0 0")
    options.addStringOption("caller-pre-arg-max-occurs", "1 1 1 1")

    options.addStringOption("caller-post-legal-args", "--spark-runner --spark-master --cluster --dry-run --java-options --conf --driver-memory --driver-cores --executor-memory --executor-cores --num-executors")
    options.addStringOption("caller-post-arg-val-types", "String String String null String file int int int int int")
    options.addStringOption("caller-post-mutex-args", "")
    options.addStringOption("caller-post-alias-args", "")
    options.addStringOption("caller-post-arg-min-occurs", "0 0 0 0 0 0 0 0 0 0")
    options.addStringOption("caller-post-arg-max-occurs", "1 1 1 1 1 1 1 1 1 1")
}



/**
 *This specifies what artifacts will be built and uploaded when performing a maven upload.
 */
artifacts {
    archives jar
    archives javadocJar
    archives sourcesJar
    archives testUtilsJar
    archives testUtilsJavadocJar
    archives testUtilsSourcesJar

}
//remove zip and tar added by the application plugin
configurations.archives.artifacts.removeAll {it.file =~ '.zip$'}
configurations.archives.artifacts.removeAll {it.file =~ '.tar$'}

/**
 * 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
}

def gatkArtifactFilter = { artifact, file -> artifact.name == 'gatk' }
def gatkTestUtilsArtifactFilter = {artifact, file -> artifact.name == 'gatk-test-utils' }
def basePomConfiguration = {
    packaging 'jar'
    description 'Development on GATK 4'
    url 'http://github.com/broadinstitute/gatk'

    scm {
        url 'scm:git@github.com:broadinstitute/gatk.git'
        connection 'scm:git@github.com:broadinstitute/gatk.git'
        developerConnection 'scm:git@github.com:broadinstitute/gatk.git'
    }

    developers {
        developer {
            id = "gatkdev"
            name = "GATK Development Team"
            email = "gatk-dev-public@broadinstitute.org"
        }
    }

    licenses {
        license {
            name 'BSD 3-Clause'
            url 'https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT'
            distribution 'repo'
        }
    }
}

install {
    install {
        repositories.mavenInstaller {
            addFilter('gatk', gatkArtifactFilter)
                    .project(basePomConfiguration)
                    .project{ name "GATK4"}
            
            addFilter('gatk-test-utils', gatkTestUtilsArtifactFilter)
                    .project(basePomConfiguration)
                    .project{ name "GATK4 Test Utilities" }
        }
    }
}
/**
 * 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 {
    doFirst {
        println "Attempting to upload version:$version"
    }
    repositories {
        mavenDeployer {
            beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }

            repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
                authentication(userName: project.findProperty("sonatypeUsername"), password: project.findProperty("sonatypePassword"))
            }

            snapshotRepository(url: "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/") {
                authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD)
            }

            addFilter('gatk-test-utils', gatkTestUtilsArtifactFilter)
                    .project(basePomConfiguration)
                    .project{ name "GATK4 Test Utilities" }

            addFilter('gatk', gatkArtifactFilter)
                    .project(basePomConfiguration)
                    .project{ name "GATK4"}

        }
    }
}

task installSpark{ dependsOn sparkJar }
task installAll{  dependsOn installSpark, installDist }

installDist.dependsOn downloadGsaLibFile

defaultTasks 'bundle'