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| import org.gradle.internal.os.OperatingSystem | |
| import javax.tools.ToolProvider | |
| buildscript { | |
| repositories { | |
| mavenCentral() | |
| } | |
| } | |
| plugins { | |
| id "java" | |
| id 'maven' | |
| id 'signing' | |
| id 'jacoco' | |
| id 'application' | |
| id 'com.palantir.git-version' version '0.5.1' | |
| id 'com.github.johnrengelman.shadow' version '1.2.3' | |
| id "com.github.kt3k.coveralls" version '2.6.3' | |
| id 'org.ajoberstar.grgit' version '1.4.2' | |
| id 'org.ajoberstar.github-pages' version '1.4.2' | |
| } | |
| mainClassName = "picard.cmdline.PicardCommandLine" | |
| repositories { | |
| mavenLocal() | |
| mavenCentral() | |
| maven { | |
| url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" //for htsjdk snapshots | |
| } | |
| } | |
| 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 = "0.7.5.201505241946" | |
| } | |
| final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.1') | |
| dependencies { | |
| compile 'com.google.guava:guava:15.0' | |
| compile 'com.github.samtools:htsjdk:' + htsjdkVersion | |
| //tools dependency for doclet requires sdk devel | |
| compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())) | |
| testCompile 'org.testng:testng:6.9.10' | |
| } | |
| sourceCompatibility = 1.8 | |
| targetCompatibility = 1.8 | |
| final isRelease = Boolean.getBoolean("release") | |
| final gitVersion = gitVersion().replaceAll(".dirty", "") | |
| version = isRelease ? gitVersion : gitVersion + "-SNAPSHOT" | |
| logger.info("build for version:" + version) | |
| group = 'com.github.broadinstitute' | |
| defaultTasks 'all' | |
| task all(dependsOn: ['jar', 'distZip', 'documentAll', 'shadowJar', 'currentJar']) | |
| jar { | |
| manifest { | |
| attributes 'Main-Class': 'picard.cmdline.PicardCommandLine', | |
| 'Implementation-Title': 'Picard', | |
| 'Implementation-Vendor': 'Broad Institute', | |
| 'Implementation-Version': version | |
| } | |
| } | |
| // 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') | |
| } | |
| } | |
| task currentJar(type: Copy){ | |
| from shadowJar | |
| into new File(buildDir, "libs") | |
| rename { string -> "picard.jar"} | |
| } | |
| shadowJar { | |
| finalizedBy currentJar | |
| } | |
| tasks.withType(Test) { | |
| outputs.upToDateWhen { false } // tests will always rerun | |
| description = "Runs the unit tests" | |
| useTestNG { | |
| if (OperatingSystem.current().isUnix()) { | |
| excludeGroups "slow", "broken" | |
| } else { | |
| excludeGroups "slow", "broken", "unix" | |
| } | |
| } | |
| // set heap size for the test JVM(s) | |
| minHeapSize = "1G" | |
| maxHeapSize = "2G" | |
| if (System.env.CI == "true") { //if running under a CI output less into the logs | |
| int count = 0 | |
| beforeTest { descriptor -> | |
| count++ | |
| if( count % 100 == 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 ) | |
| } | |
| } | |
| testLogging { | |
| testLogging { | |
| events "skipped", "failed" | |
| exceptionFormat = "full" | |
| } | |
| afterSuite { desc, result -> | |
| if (!desc.parent) { // will match the outermost suite | |
| println "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)" | |
| } | |
| } | |
| } | |
| } | |
| ext.htmlDir = new File("build/docs/html") | |
| ext.htmlDirInc = new File(htmlDir, "_includes") | |
| ext.commandClasses = ["picard.sam.AddCommentsToBam", "picard.sam.AddOrReplaceReadGroups", "picard.util.BaitDesigner", "picard.fastq.BamToBfq", | |
| "picard.sam.BamIndexStats", "picard.util.BedToIntervalList", "picard.sam.BuildBamIndex", | |
| "picard.sam.CalculateReadGroupChecksum", "picard.sam.CleanSam", "picard.analysis.CollectAlignmentSummaryMetrics", | |
| "picard.analysis.CollectBaseDistributionByCycle", "picard.analysis.CollectGcBiasMetrics", "picard.illumina.quality.CollectHiSeqXPfFailMetrics", | |
| "picard.analysis.directed.CollectHsMetrics", "picard.illumina.CollectIlluminaBasecallingMetrics", "picard.illumina.CollectIlluminaLaneMetrics", | |
| "picard.analysis.CollectInsertSizeMetrics", "picard.analysis.CollectJumpingLibraryMetrics", "picard.analysis.CollectMultipleMetrics", | |
| "picard.analysis.CollectOxoGMetrics", "picard.analysis.CollectQualityYieldMetrics", "picard.analysis.CollectRawWgsMetrics", | |
| "picard.analysis.directed.CollectTargetedPcrMetrics", "picard.analysis.CollectRnaSeqMetrics", "picard.analysis.CollectRrbsMetrics", | |
| "picard.analysis.artifacts.CollectSequencingArtifactMetrics", "picard.vcf.CollectVariantCallingMetrics", "picard.analysis.CollectWgsMetrics", | |
| "picard.analysis.CollectWgsMetricsWithNonZeroCoverage", "picard.analysis.CompareMetrics", "picard.sam.CompareSAMs", | |
| "picard.analysis.artifacts.ConvertSequencingArtifactToOxoG", "picard.sam.CreateSequenceDictionary", "picard.sam.DownsampleSam", | |
| "picard.illumina.ExtractIlluminaBarcodes", "picard.sam.markduplicates.EstimateLibraryComplexity", "picard.sam.FastqToSam", "picard.util.FifoBuffer", | |
| "picard.vcf.MendelianViolations.FindMendelianViolations","picard.fingerprint.CrosscheckFingerprints", "picard.fingerprint.ClusterCrosscheckMetrics", "picard.fingerprint.CheckFingerprint", | |
| "picard.sam.FilterSamReads", "picard.vcf.filter.FilterVcf", "picard.sam.FixMateInformation", "picard.sam.GatherBamFiles", "picard.vcf.GatherVcfs", | |
| "picard.vcf.GenotypeConcordance", "picard.illumina.IlluminaBasecallsToFastq", "picard.illumina.IlluminaBasecallsToSam", "picard.illumina.CheckIlluminaDirectory", | |
| "picard.sam.CheckTerminatorBlock", "picard.util.IntervalListTools", "picard.util.LiftOverIntervalList", "picard.vcf.LiftoverVcf", "picard.vcf.MakeSitesOnlyVcf", | |
| "picard.sam.markduplicates.MarkDuplicates", "picard.sam.markduplicates.MarkDuplicatesWithMateCigar", "picard.analysis.MeanQualityByCycle", | |
| "picard.sam.MergeBamAlignment", "picard.sam.MergeSamFiles", "picard.vcf.MergeVcfs", "picard.reference.NormalizeFasta", "picard.sam.PositionBasedDownsampleSam", | |
| "picard.reference.ExtractSequences", "picard.analysis.QualityScoreDistribution", "picard.vcf.RenameSampleInVcf", "picard.sam.ReorderSam", | |
| "picard.sam.ReplaceSamHeader", "picard.sam.RevertSam", "picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar", "picard.sam.SamFormatConverter", | |
| "picard.sam.SamToFastq", "picard.util.ScatterIntervalsByNs", "picard.sam.SetNmMdAndUqTags", | |
| "picard.sam.SortSam", "picard.vcf.SortVcf", "picard.sam.SplitSamByLibrary", "picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar", | |
| "picard.vcf.UpdateVcfSequenceDictionary", "picard.vcf.VcfFormatConverter", "picard.illumina.MarkIlluminaAdapters", "picard.vcf.SplitVcfs", | |
| "picard.sam.ValidateSamFile", "picard.sam.ViewSam", "picard.vcf.VcfToIntervalList"] | |
| //generate documentation | |
| task documentAll(dependsOn: ['documentCommands', 'createMetricsDoc', 'documentStandardOptions']){ | |
| doFirst{ | |
| htmlDirInc.mkdirs() | |
| } | |
| } | |
| task documentCommands { | |
| def previousDocTask = null | |
| def usageFile = new File(htmlDirInc, "command-line-usage.html") | |
| def sidebarFile = new File(htmlDirInc, "command-line-sidebar.html") | |
| commandClasses.each { mainClass -> | |
| task "document_${mainClass}"(type: JavaExec) { | |
| main ='picard.cmdline.CreateHtmlDocForProgram' | |
| classpath = sourceSets.main.runtimeClasspath | |
| args mainClass | |
| def outputFile = new File(htmlDirInc, mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html") | |
| doFirst { | |
| htmlDirInc.mkdirs() | |
| standardOutput = new FileOutputStream(outputFile) | |
| } | |
| outputs.file outputFile | |
| if (previousDocTask != null) delegate.dependsOn previousDocTask | |
| previousDocTask = delegate | |
| documentCommands.dependsOn(delegate) | |
| doLast { | |
| usageFile.append("{% include ${mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html"} %}") | |
| usageFile.append(System.getProperty("line.separator")) | |
| sidebarFile.append("<li><a href=\"command-line-overview.html#${mainClass.substring(mainClass.lastIndexOf(".") + 1)}\">${mainClass.substring(mainClass.lastIndexOf(".") + 1)}</a>") | |
| sidebarFile.append(System.getProperty("line.separator")) | |
| } | |
| } | |
| } | |
| outputs.dir htmlDirInc | |
| } | |
| task documentStandardOptions(type: JavaExec) { | |
| main = 'picard.cmdline.CreateHtmlDocForStandardOptions' | |
| classpath = sourceSets.main.runtimeClasspath | |
| def standardOptionsFile = new File(htmlDirInc, "standard-options.html") | |
| doFirst{ | |
| htmlDirInc.mkdirs() | |
| standardOutput = new FileOutputStream(standardOptionsFile) | |
| } | |
| outputs.file standardOptionsFile | |
| } | |
| task createMetricsDoc(dependsOn: classes, type: Javadoc) { | |
| doFirst { | |
| htmlDirInc.mkdirs() | |
| } | |
| source = sourceSets.main.allJava | |
| classpath = sourceSets.main.runtimeClasspath | |
| outputs.dir(htmlDirInc) | |
| options.destinationDirectory = htmlDirInc | |
| options.doclet = 'picard.util.MetricsDoclet' | |
| options.docletpath = sourceSets.main.runtimeClasspath.asType(List) | |
| } | |
| //end generate documentation | |
| task wrapper(type: Wrapper) { | |
| description = "Regenerate the gradle wrapper" | |
| gradleVersion = '3.1' | |
| } | |
| task javadocJar(type: Jar, dependsOn: documentAll) { | |
| classifier = 'javadoc' | |
| from 'build/docs/javadoc' | |
| } | |
| task sourcesJar(type: Jar) { | |
| from sourceSets.main.allSource | |
| classifier = 'sources' | |
| } | |
| /** | |
| * 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 { | |
| 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://artifactory.broadinstitute.org/artifactory/libs-snapshot-local/") { | |
| authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD) | |
| } | |
| pom.project { | |
| name 'Picard' | |
| packaging 'jar' | |
| description 'A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.' | |
| url 'http://broadinstitute.github.io/picard/' | |
| developers { | |
| developer { | |
| id 'picard' | |
| name 'Picard Team' | |
| url 'http://broadinstitute.github.io/picard' | |
| } | |
| } | |
| scm { | |
| url 'git@github.com:broadinstitute/picard.git' | |
| connection 'scm:git:git@github.com:broadinstitute/picard.git' | |
| } | |
| licenses { | |
| license { | |
| name 'MIT License' | |
| url 'http://opensource.org/licenses/MIT' | |
| distribution 'repo' | |
| } | |
| } | |
| } | |
| } | |
| } | |
| doFirst { | |
| System.out.println("Uploading version $version") | |
| } | |
| } | |
| //update static web docs | |
| task copyJavadoc(dependsOn: 'javadoc', type: Copy) { | |
| from 'build/docs/javadoc' | |
| into "$htmlDir/javadoc" | |
| } | |
| task updateGhPages(dependsOn: ['copyJavadoc', 'documentAll']){ | |
| outputs.dir htmlDir | |
| } | |
| updateGhPages.finalizedBy publishGhPages | |
| githubPages { | |
| repoUri = 'git@github.com:broadinstitute/picard.git' | |
| targetBranch = 'gh-pages' | |
| deleteExistingFiles = false | |
| pages { | |
| from htmlDir | |
| into '.' | |
| } | |
| } |