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Aug 3, 2016 @lbergelson adding the broad artifactory as a repository
1 import org.gradle.internal.os.OperatingSystem
2
Jun 1, 2016 @jacarey First pass at picard gradle build file.
3 import javax.tools.ToolProvider
4
5 buildscript {
6 repositories {
7 mavenCentral()
8 }
9 }
10
11 plugins {
12 id "java"
13 id 'maven'
14 id 'signing'
15 id 'jacoco'
16 id 'application'
17 id 'com.palantir.git-version' version '0.5.1'
18 id 'com.github.johnrengelman.shadow' version '1.2.3'
19 id "com.github.kt3k.coveralls" version '2.6.3'
20 id 'org.ajoberstar.grgit' version '1.4.2'
21 id 'org.ajoberstar.github-pages' version '1.4.2'
22 }
23
24 mainClassName = "picard.cmdline.PicardCommandLine"
25
26 repositories {
27 mavenLocal()
28 mavenCentral()
Aug 3, 2016 @lbergelson adding the broad artifactory as a repository
29 maven {
Jul 18, 2017 @cmnbroad Publish every snapshot build to artifactory. (#861)
30 url "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot/" //for htsjdk snapshots
Aug 3, 2016 @lbergelson adding the broad artifactory as a repository
31 }
Jun 1, 2016 @jacarey First pass at picard gradle build file.
32 }
33
34 jacocoTestReport {
35 dependsOn test
36 group = "Reporting"
37 description = "Generate Jacoco coverage reports after running tests."
38 additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
39
40 reports {
41 xml.enabled = true // coveralls plugin depends on xml format report
42 html.enabled = true
43 }
44 }
45
46 jacoco {
47 toolVersion = "0.7.5.201505241946"
48 }
49
Jun 9, 2017 @nh13 Adding the COVERED action to interval list tools. (#830)
50 final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.1')
Aug 3, 2016 @lbergelson letting htsjdk version be specified on command line
51
Jun 1, 2016 @jacarey First pass at picard gradle build file.
52 dependencies {
Jul 31, 2017 @danxmoran Bump GKL version to avoid hanging in AVX support check. (#888)
53 compile('com.intel.gkl:gkl:0.5.3') {
Jul 1, 2017 @danxmoran Make sure the GKL isn't evicting our htsjdk version.
54 exclude module: 'htsjdk'
55 }
Jun 1, 2016 @jacarey First pass at picard gradle build file.
56 compile 'com.google.guava:guava:15.0'
Aug 3, 2016 @lbergelson letting htsjdk version be specified on command line
57 compile 'com.github.samtools:htsjdk:' + htsjdkVersion
Jun 1, 2016 @jacarey First pass at picard gradle build file.
58 //tools dependency for doclet requires sdk devel
59 compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
60 testCompile 'org.testng:testng:6.9.10'
Jul 1, 2017 @danxmoran Add test verifying Intel Inflater/Deflater can be loaded.
61 testCompile 'org.apache.commons:commons-lang3:3.6'
Jun 1, 2016 @jacarey First pass at picard gradle build file.
62 }
63
Jul 1, 2017 @danxmoran Make sure the GKL isn't evicting our htsjdk version.
64 configurations.all {
65 resolutionStrategy {
66 // force the htsjdk version so we don't get a different one transitively
67 force 'com.github.samtools:htsjdk:' + htsjdkVersion
68 }
Jun 1, 2016 @jacarey First pass at picard gradle build file.
69 }
70
71 sourceCompatibility = 1.8
72 targetCompatibility = 1.8
73
74 final isRelease = Boolean.getBoolean("release")
75 final gitVersion = gitVersion().replaceAll(".dirty", "")
76 version = isRelease ? gitVersion : gitVersion + "-SNAPSHOT"
77
78 logger.info("build for version:" + version)
79 group = 'com.github.broadinstitute'
80
81 defaultTasks 'all'
82
Aug 5, 2016 @lbergelson creating a picard.jar when running ./gradlew (#618)
83 task all(dependsOn: ['jar', 'distZip', 'documentAll', 'shadowJar', 'currentJar'])
Jun 1, 2016 @jacarey First pass at picard gradle build file.
84
85 jar {
86 manifest {
87 attributes 'Main-Class': 'picard.cmdline.PicardCommandLine',
88 'Implementation-Title': 'Picard',
89 'Implementation-Vendor': 'Broad Institute',
90 'Implementation-Version': version
91 }
92 }
93 // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
94 if (JavaVersion.current().isJava8Compatible()) {
95 tasks.withType(Javadoc) {
96 options.addStringOption('Xdoclint:none', '-quiet')
97 }
98 }
99
Aug 5, 2016 @lbergelson creating a picard.jar when running ./gradlew (#618)
100 task currentJar(type: Copy){
101 from shadowJar
102 into new File(buildDir, "libs")
103 rename { string -> "picard.jar"}
104 }
105
106 shadowJar {
107 finalizedBy currentJar
108 }
109
Jun 1, 2016 @jacarey First pass at picard gradle build file.
110 tasks.withType(Test) {
111 outputs.upToDateWhen { false } // tests will always rerun
112 description = "Runs the unit tests"
113
114 useTestNG {
115 if (OperatingSystem.current().isUnix()) {
116 excludeGroups "slow", "broken"
117 } else {
118 excludeGroups "slow", "broken", "unix"
119 }
120 }
121
122 // set heap size for the test JVM(s)
123 minHeapSize = "1G"
124 maxHeapSize = "2G"
125 if (System.env.CI == "true") { //if running under a CI output less into the logs
126 int count = 0
127
128 beforeTest { descriptor ->
129 count++
130 if( count % 100 == 0) {
131 logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
132 }
133 }
134 } else {
135 // show standard out and standard error of the test JVM(s) on the console
136 testLogging.showStandardStreams = true
137 beforeTest { descriptor ->
138 logger.lifecycle("Running Test: " + descriptor)
139 }
140
141 // listen to standard out and standard error of the test JVM(s)
142 onOutput { descriptor, event ->
143 logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
144 }
145 }
146
147 testLogging {
148 testLogging {
149 events "skipped", "failed"
150 exceptionFormat = "full"
151 }
152 afterSuite { desc, result ->
153 if (!desc.parent) { // will match the outermost suite
154 println "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
155 }
156 }
157 }
158 }
159
160 ext.htmlDir = new File("build/docs/html")
161 ext.htmlDirInc = new File(htmlDir, "_includes")
162 ext.commandClasses = ["picard.sam.AddCommentsToBam", "picard.sam.AddOrReplaceReadGroups", "picard.util.BaitDesigner", "picard.fastq.BamToBfq",
Apr 25, 2017 @ronlevine Remove deprecated classes
163 "picard.sam.BamIndexStats", "picard.util.BedToIntervalList", "picard.sam.BuildBamIndex",
Jun 1, 2016 @jacarey First pass at picard gradle build file.
164 "picard.sam.CalculateReadGroupChecksum", "picard.sam.CleanSam", "picard.analysis.CollectAlignmentSummaryMetrics",
165 "picard.analysis.CollectBaseDistributionByCycle", "picard.analysis.CollectGcBiasMetrics", "picard.illumina.quality.CollectHiSeqXPfFailMetrics",
166 "picard.analysis.directed.CollectHsMetrics", "picard.illumina.CollectIlluminaBasecallingMetrics", "picard.illumina.CollectIlluminaLaneMetrics",
167 "picard.analysis.CollectInsertSizeMetrics", "picard.analysis.CollectJumpingLibraryMetrics", "picard.analysis.CollectMultipleMetrics",
168 "picard.analysis.CollectOxoGMetrics", "picard.analysis.CollectQualityYieldMetrics", "picard.analysis.CollectRawWgsMetrics",
169 "picard.analysis.directed.CollectTargetedPcrMetrics", "picard.analysis.CollectRnaSeqMetrics", "picard.analysis.CollectRrbsMetrics",
170 "picard.analysis.artifacts.CollectSequencingArtifactMetrics", "picard.vcf.CollectVariantCallingMetrics", "picard.analysis.CollectWgsMetrics",
171 "picard.analysis.CollectWgsMetricsWithNonZeroCoverage", "picard.analysis.CompareMetrics", "picard.sam.CompareSAMs",
172 "picard.analysis.artifacts.ConvertSequencingArtifactToOxoG", "picard.sam.CreateSequenceDictionary", "picard.sam.DownsampleSam",
173 "picard.illumina.ExtractIlluminaBarcodes", "picard.sam.markduplicates.EstimateLibraryComplexity", "picard.sam.FastqToSam", "picard.util.FifoBuffer",
Jun 27, 2017 @yfarjoun Include tumor-aware results when results have been rolled-up (sample …
174 "picard.vcf.MendelianViolations.FindMendelianViolations","picard.fingerprint.CrosscheckFingerprints", "picard.fingerprint.ClusterCrosscheckMetrics", "picard.fingerprint.CheckFingerprint",
Jun 1, 2016 @jacarey First pass at picard gradle build file.
175 "picard.sam.FilterSamReads", "picard.vcf.filter.FilterVcf", "picard.sam.FixMateInformation", "picard.sam.GatherBamFiles", "picard.vcf.GatherVcfs",
176 "picard.vcf.GenotypeConcordance", "picard.illumina.IlluminaBasecallsToFastq", "picard.illumina.IlluminaBasecallsToSam", "picard.illumina.CheckIlluminaDirectory",
177 "picard.sam.CheckTerminatorBlock", "picard.util.IntervalListTools", "picard.util.LiftOverIntervalList", "picard.vcf.LiftoverVcf", "picard.vcf.MakeSitesOnlyVcf",
178 "picard.sam.markduplicates.MarkDuplicates", "picard.sam.markduplicates.MarkDuplicatesWithMateCigar", "picard.analysis.MeanQualityByCycle",
179 "picard.sam.MergeBamAlignment", "picard.sam.MergeSamFiles", "picard.vcf.MergeVcfs", "picard.reference.NormalizeFasta", "picard.sam.PositionBasedDownsampleSam",
180 "picard.reference.ExtractSequences", "picard.analysis.QualityScoreDistribution", "picard.vcf.RenameSampleInVcf", "picard.sam.ReorderSam",
181 "picard.sam.ReplaceSamHeader", "picard.sam.RevertSam", "picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar", "picard.sam.SamFormatConverter",
Nov 30, 2016 @vdauwera Add tools to be documented + minor tweaks to MD docs
182 "picard.sam.SamToFastq", "picard.util.ScatterIntervalsByNs", "picard.sam.SetNmMdAndUqTags",
183 "picard.sam.SortSam", "picard.vcf.SortVcf", "picard.sam.SplitSamByLibrary", "picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar",
Jun 1, 2016 @jacarey First pass at picard gradle build file.
184 "picard.vcf.UpdateVcfSequenceDictionary", "picard.vcf.VcfFormatConverter", "picard.illumina.MarkIlluminaAdapters", "picard.vcf.SplitVcfs",
185 "picard.sam.ValidateSamFile", "picard.sam.ViewSam", "picard.vcf.VcfToIntervalList"]
186
187 //generate documentation
188
189 task documentAll(dependsOn: ['documentCommands', 'createMetricsDoc', 'documentStandardOptions']){
190 doFirst{
191 htmlDirInc.mkdirs()
192 }
193 }
194
195 task documentCommands {
196 def previousDocTask = null
197 def usageFile = new File(htmlDirInc, "command-line-usage.html")
198 def sidebarFile = new File(htmlDirInc, "command-line-sidebar.html")
199
200 commandClasses.each { mainClass ->
201 task "document_${mainClass}"(type: JavaExec) {
202 main ='picard.cmdline.CreateHtmlDocForProgram'
203 classpath = sourceSets.main.runtimeClasspath
204 args mainClass
205 def outputFile = new File(htmlDirInc, mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html")
206 doFirst {
207 htmlDirInc.mkdirs()
208 standardOutput = new FileOutputStream(outputFile)
209 }
210 outputs.file outputFile
211
212 if (previousDocTask != null) delegate.dependsOn previousDocTask
213 previousDocTask = delegate
214 documentCommands.dependsOn(delegate)
215 doLast {
216 usageFile.append("{% include ${mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html"} %}")
217 usageFile.append(System.getProperty("line.separator"))
218 sidebarFile.append("<li><a href=\"command-line-overview.html#${mainClass.substring(mainClass.lastIndexOf(".") + 1)}\">${mainClass.substring(mainClass.lastIndexOf(".") + 1)}</a>")
219 sidebarFile.append(System.getProperty("line.separator"))
220 }
221 }
222 }
223 outputs.dir htmlDirInc
224 }
225
226 task documentStandardOptions(type: JavaExec) {
227 main = 'picard.cmdline.CreateHtmlDocForStandardOptions'
228 classpath = sourceSets.main.runtimeClasspath
229 def standardOptionsFile = new File(htmlDirInc, "standard-options.html")
230 doFirst{
231 htmlDirInc.mkdirs()
232 standardOutput = new FileOutputStream(standardOptionsFile)
233 }
234 outputs.file standardOptionsFile
235 }
236
Feb 9, 2017 @lbergelson fix createMetricsDoclet gradle task (#749)
237 task createMetricsDoc(dependsOn: classes, type: Javadoc) {
238 doFirst {
239 htmlDirInc.mkdirs()
240 }
Jul 31, 2017 @danxmoran Bump GKL version to avoid hanging in AVX support check. (#888)
241
Jun 1, 2016 @jacarey First pass at picard gradle build file.
242 source = sourceSets.main.allJava
243 classpath = sourceSets.main.runtimeClasspath
Feb 9, 2017 @lbergelson fix createMetricsDoclet gradle task (#749)
244 outputs.dir(htmlDirInc)
245
246 options.destinationDirectory = htmlDirInc
Jun 1, 2016 @jacarey First pass at picard gradle build file.
247 options.doclet = 'picard.util.MetricsDoclet'
248 options.docletpath = sourceSets.main.runtimeClasspath.asType(List)
249 }
250 //end generate documentation
251
252 task wrapper(type: Wrapper) {
253 description = "Regenerate the gradle wrapper"
Nov 7, 2016 @lbergelson updating gradle from 2.13 -> 3.1 (#680)
254 gradleVersion = '3.1'
Jun 1, 2016 @jacarey First pass at picard gradle build file.
255 }
256
257 task javadocJar(type: Jar, dependsOn: documentAll) {
258 classifier = 'javadoc'
259 from 'build/docs/javadoc'
260 }
261
262 task sourcesJar(type: Jar) {
263 from sourceSets.main.allSource
264 classifier = 'sources'
265 }
266
267 /**
268 * This specifies what artifacts will be built and uploaded when performing a maven upload.
269 */
270 artifacts {
271 archives jar
272 archives javadocJar
273 archives sourcesJar
274 }
275
276 /**
277 * Sign non-snapshot releases with our secret key. This should never need to be invoked directly.
278 */
279 signing {
280 required { isRelease && gradle.taskGraph.hasTask("uploadArchives") }
281 sign configurations.archives
282 }
283
284 /**
285 * Upload a release to sonatype. You must be an authorized uploader and have your sonatype
286 * username and password information in your gradle properties file. See the readme for more info.
287 *
288 * For releasing to your local maven repo, use gradle install
289 */
290 uploadArchives {
291 repositories {
292 mavenDeployer {
293 beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }
294
295 repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
296 authentication(userName: project.findProperty("sonatypeUsername"), password: project.findProperty("sonatypePassword"))
297 }
298
Jul 18, 2017 @cmnbroad Publish every snapshot build to artifactory. (#861)
299 snapshotRepository(url: "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/") {
Jun 1, 2016 @jacarey First pass at picard gradle build file.
300 authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD)
301 }
302
303 pom.project {
304 name 'Picard'
305 packaging 'jar'
306 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.'
307 url 'http://broadinstitute.github.io/picard/'
308
309 developers {
310 developer {
311 id 'picard'
312 name 'Picard Team'
313 url 'http://broadinstitute.github.io/picard'
314 }
315 }
316
317 scm {
318 url 'git@github.com:broadinstitute/picard.git'
319 connection 'scm:git:git@github.com:broadinstitute/picard.git'
320 }
321
322 licenses {
323 license {
324 name 'MIT License'
325 url 'http://opensource.org/licenses/MIT'
326 distribution 'repo'
327 }
328 }
329 }
330 }
331 }
332 doFirst {
333 System.out.println("Uploading version $version")
334 }
335 }
336
337 //update static web docs
338 task copyJavadoc(dependsOn: 'javadoc', type: Copy) {
339 from 'build/docs/javadoc'
340 into "$htmlDir/javadoc"
341 }
342
343 task updateGhPages(dependsOn: ['copyJavadoc', 'documentAll']){
344 outputs.dir htmlDir
345 }
346
347 updateGhPages.finalizedBy publishGhPages
348
349 githubPages {
350 repoUri = 'git@github.com:broadinstitute/picard.git'
351 targetBranch = 'gh-pages'
352 deleteExistingFiles = false
353 pages {
354 from htmlDir
355 into '.'
356 }
357 }