2014-01-30 06:00:06 +08:00
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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<!--
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This pom is the aggregator for all sting/gatk poms
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See also:
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http://maven.apache.org/pom.html#Inheritance_v
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http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
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http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
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-->
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<parent>
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<groupId>org.broadinstitute.sting</groupId>
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<artifactId>sting-root</artifactId>
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<version>2.6-SNAPSHOT</version>
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<relativePath>public/sting-root</relativePath>
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</parent>
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<artifactId>sting-aggregator</artifactId>
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<packaging>pom</packaging>
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<name>Sting Aggregator</name>
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<modules>
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<module>public</module>
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<!-- private & protected optionally enabled as profiles -->
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</modules>
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<properties>
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<sting.basedir>${project.basedir}</sting.basedir>
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<resource.bundle.path>StingText.properties</resource.bundle.path>
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<resource.bundle.skip>false</resource.bundle.skip>
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<!-- TODO: Need a better a way to say "don't include hidden" by default -->
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<gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
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<sting.jar.phase>package</sting.jar.phase>
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<sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
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<sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
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<sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
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<sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
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<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
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</properties>
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<dependencies>
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<dependency>
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<groupId>com.sun</groupId>
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<artifactId>tools</artifactId>
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</dependency>
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</dependencies>
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<build>
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<!-- Plugin configuration -->
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<pluginManagement>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-clean-plugin</artifactId>
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<configuration>
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<filesets>
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<!--
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TODO: Once GATKDoclet stops hard coding paths, we remove this and leave
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TODO: it to the standard maven conventions to clean up for us
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-->
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<fileset>
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<directory>gatkdocs</directory>
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</fileset>
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<fileset>
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<directory>${basedir}</directory>
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<includes>
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<include>javadoc.sh</include>
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<include>options</include>
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<include>packages</include>
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</includes>
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</fileset>
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<!--
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Shade dumps this temp file in basedir, with no good way to reconfigure.
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https://jira.codehaus.org/browse/MSHADE-145
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-->
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<fileset>
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<directory>${basedir}</directory>
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<includes>
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<include>dependency-reduced-pom.xml</include>
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</includes>
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</fileset>
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</filesets>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-dependency-plugin</artifactId>
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<executions>
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<execution>
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<id>unpack-direct-dependencies</id>
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<goals>
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<goal>unpack-dependencies</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<excludeTransitive>true</excludeTransitive>
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<outputDirectory>${project.build.outputDirectory}</outputDirectory>
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<includeTypes>jar</includeTypes>
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<excludeScope>system</excludeScope>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- TODO: Change the ResourceBundleExtractorDoclet to not require log4j.properties file -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<executions>
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<execution>
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<id>copy-resource-bundle-log4j</id>
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<goals>
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<goal>copy-resources</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<outputDirectory>${project.reporting.outputDirectory}/apidocs</outputDirectory>
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<resources>
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<resource>
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<directory>${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help</directory>
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</resource>
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</resources>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<executions>
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<execution>
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<id>extract-resource-bundle</id>
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<goals>
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<goal>javadoc</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<!-- Allow skipping for "fasttest" -->
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<skip>${resource.bundle.skip}</skip>
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<doclet>org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet</doclet>
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<!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
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<docletPath>${project.build.outputDirectory}</docletPath>
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<docletArtifact>
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<groupId>${project.groupId}</groupId>
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<!-- TODO: THIS IS SUPPOSED TO BE STING-UTILS! -->
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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</docletArtifact>
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<maxmemory>2g</maxmemory>
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<useStandardDocletOptions>false</useStandardDocletOptions>
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<quiet>true</quiet>
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<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} -out ${project.build.outputDirectory}/${resource.bundle.path}</additionalparam>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<proc>none</proc>
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<annotationProcessors>
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<annotationProcessor>com.google.java.contract.core.apt.AnnotationProcessor</annotationProcessor>
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</annotationProcessors>
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<compilerArguments>
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<!--
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For com.sun.istack.internal. Because bootclasspath is set to include rt.jar, now jce.jar must be set for the Oracle only javax.crypto also.
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TODO: This Sun internal tool usage needs to be removed ASAP!
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-->
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<bootclasspath>${java.home}/lib/rt.jar:${java.home}/lib/jce.jar</bootclasspath>
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</compilerArguments>
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</configuration>
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<executions>
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<execution>
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<id>default-compile</id>
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<phase>none</phase>
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</execution>
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<execution>
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<id>default-testCompile</id>
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<phase>none</phase>
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</execution>
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<!--
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Explicit package-info creation to match existing ant output.
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-->
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<execution>
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<id>compile-package-info</id>
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<goals>
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<goal>compile</goal>
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</goals>
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<phase>compile</phase>
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<configuration>
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<compilerArgs>
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<arg>-Xpkginfo:always</arg>
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</compilerArgs>
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<includes>
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<include>**/package-info.java</include>
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</includes>
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</configuration>
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</execution>
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<!--
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TODO: Currently disabled in build.xml. Here as well.
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<execution>
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<id>compile-annotations</id>
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<phase>compile</phase>
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<goals>
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<goal>compile</goal>
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</goals>
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<configuration>
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<proc>only</proc>
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</configuration>
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</execution>
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-->
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<execution>
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<id>compile-java</id>
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<goals>
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<goal>compile</goal>
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</goals>
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<phase>compile</phase>
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<configuration>
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<!--
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Package info is supposed to be in source:
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http://maven.apache.org/plugins/maven-javadoc-plugin/examples/javadoc-resources.html
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But maven-compile-plugin doesn't auto exclude these:
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https://jira.codehaus.org/browse/MCOMPILER-205?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=326505#comment-326505
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So, explicitly exclude them
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-->
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<excludes>
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<exclude>**/package-info.java</exclude>
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</excludes>
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</configuration>
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</execution>
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<!--
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TODO: Currently disabled in build.xml. Here as well.
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<execution>
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<id>testCompile-annotations</id>
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<phase>test-compile</phase>
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<goals>
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<goal>testCompile</goal>
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</goals>
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<configuration>
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<proc>only</proc>
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</configuration>
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</execution>
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-->
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<execution>
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<id>testCompile-java</id>
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<goals>
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<goal>testCompile</goal>
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</goals>
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<phase>test-compile</phase>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.scala-tools</groupId>
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<artifactId>maven-scala-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>compile</goal>
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<goal>testCompile</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<executions>
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<execution>
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<id>default-jar</id>
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<phase>${sting.jar.phase}</phase>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<executions>
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<execution>
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<id>sting-executable</id>
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<goals>
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<goal>shade</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<minimizeJar>true</minimizeJar>
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<artifactSet>
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<excludes>
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<exclude>org.broadinstitute.sting:gsalib:tar.gz:*</exclude>
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<exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
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</excludes>
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</artifactSet>
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<transformers>
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<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
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<manifestEntries>
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<Main-Class>${app.main.class}</Main-Class>
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</manifestEntries>
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</transformer>
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<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
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<resource>${resource.bundle.path}</resource>
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</transformer>
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</transformers>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<executions>
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<execution>
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<id>example-resources</id>
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<goals>
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<goal>single</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<descriptors>
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<descriptor>src/main/assembly/example-resources.xml</descriptor>
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</descriptors>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>binary-dist</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>single</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<descriptors>
|
|
|
|
|
<descriptor>src/main/assembly/binary-dist.xml</descriptor>
|
|
|
|
|
</descriptors>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
</executions>
|
|
|
|
|
</plugin>
|
|
|
|
|
|
|
|
|
|
<!-- TODO: Remove temporary symbolic link creation, after fixing test paths to use local resources. -->
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>com.pyx4j</groupId>
|
|
|
|
|
<artifactId>maven-junction-plugin</artifactId>
|
|
|
|
|
<executions>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-public-testdata</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>link</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/public/testdata</dst>
|
|
|
|
|
<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>unlink-public-testdata</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>unlink</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/public/testdata</dst>
|
|
|
|
|
<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-private-testdata</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>link</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/private/testdata</dst>
|
|
|
|
|
<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>unlink-private-testdata</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>unlink</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/private/testdata</dst>
|
|
|
|
|
<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-public-qscript</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>link</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/public/scala/qscript</dst>
|
|
|
|
|
<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>unlink-public-qscript</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>unlink</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/public/scala/qscript</dst>
|
|
|
|
|
<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-private-qscript</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>link</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/private/scala/qscript</dst>
|
|
|
|
|
<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>unlink-private-qscript</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>unlink</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${basedir}/private/scala/qscript</dst>
|
|
|
|
|
<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-git-release</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>link</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<links>
|
|
|
|
|
<link>
|
|
|
|
|
<dst>${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2</dst>
|
|
|
|
|
<src>${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2</src>
|
|
|
|
|
</link>
|
|
|
|
|
</links>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
</executions>
|
|
|
|
|
</plugin>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>org.apache.maven.plugins</groupId>
|
|
|
|
|
<artifactId>maven-invoker-plugin</artifactId>
|
|
|
|
|
<configuration>
|
|
|
|
|
<skipInvocation>true</skipInvocation>
|
|
|
|
|
<debug>false</debug>
|
|
|
|
|
<pom>${sting.basedir}/public/package-tests/pom.xml</pom>
|
|
|
|
|
<noLog>true</noLog>
|
|
|
|
|
<streamLogs>true</streamLogs>
|
|
|
|
|
<localRepositoryPath>${sting.basedir}/${maven.repo.local}</localRepositoryPath>
|
|
|
|
|
<properties>
|
|
|
|
|
<test>${test}</test>
|
|
|
|
|
<it.test>${it.test}</it.test>
|
|
|
|
|
<skip>false</skip>
|
|
|
|
|
<maven.test.skip>false</maven.test.skip>
|
|
|
|
|
<sting.packagetests.artifactId>${sting.packagetests.artifactId}</sting.packagetests.artifactId>
|
|
|
|
|
<sting.packagetests.testClasses>${project.build.testOutputDirectory}</sting.packagetests.testClasses>
|
|
|
|
|
<sting.packagetests.basedir>${project.basedir}</sting.packagetests.basedir>
|
|
|
|
|
<sting.pipelinetests.run>${sting.pipelinetests.run}</sting.pipelinetests.run>
|
|
|
|
|
<maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
|
|
|
|
|
<maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
|
|
|
|
|
</properties>
|
|
|
|
|
</configuration>
|
|
|
|
|
<executions>
|
2014-01-30 17:47:54 +08:00
|
|
|
<!--
|
|
|
|
|
TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
|
|
|
|
|
-->
|
2014-01-30 06:00:06 +08:00
|
|
|
<execution>
|
|
|
|
|
<id>package-unittests</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>run</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<configuration>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>test</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
|
|
|
|
|
<properties>
|
2014-01-30 17:47:54 +08:00
|
|
|
<unittests.profile.enabled>true</unittests.profile.enabled>
|
|
|
|
|
<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
|
2014-01-30 06:00:06 +08:00
|
|
|
<sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
|
|
|
|
|
</properties>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>package-integrationtests</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>integration-test</goal>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<configuration>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
|
|
|
|
|
<properties>
|
2014-01-30 17:47:54 +08:00
|
|
|
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
|
|
|
|
|
<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
|
2014-01-30 06:00:06 +08:00
|
|
|
<sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
|
|
|
|
|
</properties>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>package-pipelinetests</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>integration-test</goal>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<configuration>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
|
|
|
|
|
<properties>
|
2014-01-30 17:47:54 +08:00
|
|
|
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
|
|
|
|
|
<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
|
2014-01-30 06:00:06 +08:00
|
|
|
<sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
|
|
|
|
|
</properties>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>package-largescaletests</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>integration-test</goal>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<configuration>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>verify</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
|
|
|
|
|
<properties>
|
2014-01-30 17:47:54 +08:00
|
|
|
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
|
|
|
|
|
<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
|
2014-01-30 06:00:06 +08:00
|
|
|
<sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
|
|
|
|
|
</properties>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
</executions>
|
|
|
|
|
</plugin>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>org.apache.maven.plugins</groupId>
|
|
|
|
|
<artifactId>maven-install-plugin</artifactId>
|
|
|
|
|
<version>2.5</version>
|
|
|
|
|
<executions>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>install-package</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>install-file</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>none</phase>
|
|
|
|
|
<configuration>
|
|
|
|
|
<generatePom>true</generatePom>
|
|
|
|
|
<groupId>${project.groupId}</groupId>
|
|
|
|
|
<artifactId>${project.artifactId}</artifactId>
|
|
|
|
|
<version>${project.version}</version>
|
|
|
|
|
<packaging>${project.packaging}</packaging>
|
|
|
|
|
<file>${project.build.directory}/${project.build.finalName}.${project.packaging}</file>
|
|
|
|
|
</configuration>
|
|
|
|
|
</execution>
|
|
|
|
|
</executions>
|
|
|
|
|
</plugin>
|
|
|
|
|
</plugins>
|
|
|
|
|
</pluginManagement>
|
|
|
|
|
|
|
|
|
|
<!-- Invoke plugins that always run -->
|
|
|
|
|
<plugins>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>org.apache.maven.plugins</groupId>
|
|
|
|
|
<artifactId>maven-failsafe-plugin</artifactId>
|
|
|
|
|
</plugin>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>com.pyx4j</groupId>
|
|
|
|
|
<artifactId>maven-junction-plugin</artifactId>
|
|
|
|
|
<executions>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>link-public-testdata</id>
|
|
|
|
|
<phase>process-test-resources</phase>
|
|
|
|
|
</execution>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>unlink-public-testdata</id>
|
|
|
|
|
<phase>clean</phase>
|
|
|
|
|
</execution>
|
|
|
|
|
</executions>
|
|
|
|
|
</plugin>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>org.apache.maven.plugins</groupId>
|
|
|
|
|
<artifactId>maven-clean-plugin</artifactId>
|
|
|
|
|
</plugin>
|
|
|
|
|
<plugin>
|
|
|
|
|
<groupId>com.google.code.sortpom</groupId>
|
|
|
|
|
<artifactId>maven-sortpom-plugin</artifactId>
|
|
|
|
|
<executions>
|
|
|
|
|
<execution>
|
|
|
|
|
<id>package-tests</id>
|
|
|
|
|
<goals>
|
|
|
|
|
<goal>sort</goal>
|
|
|
|
|
</goals>
|
|
|
|
|
<phase>verify</phase>
|
|
|
|
|
<inherited>false</inherited>
|
|
|
|
|
<configuration>
|
|
|
|
|
<pomFile>public/package-tests/pom.xml</pomFile>
|
|
|
|
|
</configuration>
|
|
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<reporting>
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<plugins>
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|
<plugin>
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|
<groupId>org.apache.maven.plugins</groupId>
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|
<artifactId>maven-javadoc-plugin</artifactId>
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<version>2.9.1</version>
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|
|
<reportSets>
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|
<!-- By not specifying an id, shut off all default javadocs from mvn site -->
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|
<reportSet>
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|
<reports />
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</reportSet>
|
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|
|
|
<reportSet>
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|
|
|
|
<id>generate-gatk-docs</id>
|
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|
|
|
<reports>
|
|
|
|
|
<report>aggregate</report>
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|
|
|
|
</reports>
|
|
|
|
|
<!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
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|
|
|
|
<inherited>false</inherited>
|
|
|
|
|
<configuration>
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|
|
|
|
<doclet>org.broadinstitute.sting.utils.help.GATKDoclet</doclet>
|
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|
|
<docletArtifact>
|
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|
|
<groupId>${project.groupId}</groupId>
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|
|
|
<artifactId>gatk-package</artifactId>
|
|
|
|
|
<version>${project.version}</version>
|
|
|
|
|
</docletArtifact>
|
|
|
|
|
<useStandardDocletOptions>false</useStandardDocletOptions>
|
|
|
|
|
<quiet>true</quiet>
|
|
|
|
|
<show>private</show>
|
|
|
|
|
<!--
|
|
|
|
|
TODO: Stop GATKDoclet from hardcoding paths and start using parameters.
|
|
|
|
|
For now... just run from the base directory, target/site/../..
|
|
|
|
|
-->
|
|
|
|
|
<destDir>../..</destDir>
|
|
|
|
|
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden}</additionalparam>
|
|
|
|
|
<!--
|
|
|
|
|
TODO: Leaving this true applies a patch to the git commited file
|
|
|
|
|
TODO: private/resources/clover/api/index.html
|
|
|
|
|
TODO: Determine if this file was generated and shoudldn't be touched,
|
|
|
|
|
TODO: or patch the file and commit a new version.
|
|
|
|
|
-->
|
|
|
|
|
<applyJavadocSecurityFix>false</applyJavadocSecurityFix>
|
|
|
|
|
</configuration>
|
|
|
|
|
</reportSet>
|
|
|
|
|
</reportSets>
|
|
|
|
|
</plugin>
|
|
|
|
|
</plugins>
|
|
|
|
|
</reporting>
|
|
|
|
|
|
|
|
|
|
<profiles>
|
|
|
|
|
<!-- Optionally include protected -->
|
|
|
|
|
<profile>
|
|
|
|
|
<id>protected</id>
|
|
|
|
|
<activation>
|
|
|
|
|
<file>
|
|
|
|
|
<exists>${basedir}/protected/pom.xml</exists>
|
|
|
|
|
</file>
|
|
|
|
|
</activation>
|
|
|
|
|
<modules>
|
|
|
|
|
<module>protected</module>
|
|
|
|
|
</modules>
|
|
|
|
|
</profile>
|
|
|
|
|
|
|
|
|
|
<!-- Optionally include private -->
|
|
|
|
|
<profile>
|
|
|
|
|
<id>private</id>
|
|
|
|
|
<activation>
|
|
|
|
|
<file>
|
|
|
|
|
<exists>${basedir}/private/pom.xml</exists>
|
|
|
|
|
</file>
|
|
|
|
|
</activation>
|
|
|
|
|
<modules>
|
|
|
|
|
<module>private</module>
|
|
|
|
|
</modules>
|
|
|
|
|
</profile>
|
|
|
|
|
</profiles>
|
|
|
|
|
|
|
|
|
|
</project>
|
