Added maven pom.xmls for various artifacts.
This commit is contained in:
Khalid Shakir
David Roazen
parent
d1a689af33
commit
caa76cdac4
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@ -0,0 +1,733 @@
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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>
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</configuration>
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</execution>
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<execution>
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<id>binary-dist</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/binary-dist.xml</descriptor>
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</descriptors>
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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: Remove temporary symbolic link creation, after fixing test paths to use local resources. -->
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<plugin>
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<groupId>com.pyx4j</groupId>
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<artifactId>maven-junction-plugin</artifactId>
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<executions>
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<execution>
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<id>link-public-testdata</id>
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<goals>
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<goal>link</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/public/testdata</dst>
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<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>unlink-public-testdata</id>
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<goals>
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<goal>unlink</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/public/testdata</dst>
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<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>link-private-testdata</id>
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<goals>
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<goal>link</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/private/testdata</dst>
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<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>unlink-private-testdata</id>
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<goals>
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<goal>unlink</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/private/testdata</dst>
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<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>link-public-qscript</id>
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<goals>
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<goal>link</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/public/scala/qscript</dst>
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<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>unlink-public-qscript</id>
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<goals>
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<goal>unlink</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/public/scala/qscript</dst>
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<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>link-private-qscript</id>
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<goals>
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<goal>link</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/private/scala/qscript</dst>
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<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>unlink-private-qscript</id>
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<goals>
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<goal>unlink</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${basedir}/private/scala/qscript</dst>
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<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
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</link>
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</links>
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</configuration>
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</execution>
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<execution>
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<id>link-git-release</id>
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<goals>
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<goal>link</goal>
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</goals>
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<phase>none</phase>
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<configuration>
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<links>
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<link>
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<dst>${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2</dst>
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<src>${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2</src>
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</link>
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</links>
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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-invoker-plugin</artifactId>
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||||
<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>${maven.failsafe.debug}</maven.failsafe.debug>
|
||||
</properties>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>package-unittests</id>
|
||||
<goals>
|
||||
<goal>run</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<goals>
|
||||
<goal>test</goal>
|
||||
</goals>
|
||||
<profiles>
|
||||
<profile>unittests</profile>
|
||||
</profiles>
|
||||
<skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
|
||||
<properties>
|
||||
<sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
|
||||
</properties>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-integrationtests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<profiles>
|
||||
<profile>integrationtests</profile>
|
||||
</profiles>
|
||||
<skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
|
||||
<properties>
|
||||
<sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
|
||||
</properties>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-pipelinetests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<profiles>
|
||||
<profile>integrationtests</profile>
|
||||
</profiles>
|
||||
<skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
|
||||
<properties>
|
||||
<sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
|
||||
</properties>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-largescaletests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<profiles>
|
||||
<profile>integrationtests</profile>
|
||||
</profiles>
|
||||
<skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
|
||||
<properties>
|
||||
<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>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<reporting>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<version>2.9.1</version>
|
||||
<reportSets>
|
||||
<!-- By not specifying an id, shut off all default javadocs from mvn site -->
|
||||
<reportSet>
|
||||
<reports />
|
||||
</reportSet>
|
||||
<reportSet>
|
||||
<id>generate-gatk-docs</id>
|
||||
<reports>
|
||||
<report>aggregate</report>
|
||||
</reports>
|
||||
<!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
|
||||
<inherited>false</inherited>
|
||||
<configuration>
|
||||
<doclet>org.broadinstitute.sting.utils.help.GATKDoclet</doclet>
|
||||
<docletArtifact>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-package</artifactId>
|
||||
<version>${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>${basedir}/private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<modules>
|
||||
<module>private</module>
|
||||
</modules>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,144 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>gatk-protected</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>GATK Protected</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>net.sf.jgrapht</groupId>
|
||||
<artifactId>jgrapht</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>gov.nist</groupId>
|
||||
<artifactId>Jama</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>it.unimi.dsi</groupId>
|
||||
<artifactId>fastutil</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>sting-utils</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.caliper</groupId>
|
||||
<artifactId>caliper</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-resource-bundle-log4j</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>extract-resource-bundle</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-invoker-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>package-unittests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-integrationtests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-largescaletests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-pipelinetests</id>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>private</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- TODO: All tests require access to private. For now. -->
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-private-testdata</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-testdata</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-root</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../public/sting-root</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>sting-protected</artifactId>
|
||||
<packaging>pom</packaging>
|
||||
<name>Sting Protected</name>
|
||||
|
||||
<modules>
|
||||
<module>gatk-protected</module>
|
||||
</modules>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/..</sting.basedir>
|
||||
</properties>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,257 @@
|
|||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<!-- Properties for your assembly -->
|
||||
<groupId>org.mycompany.app</groupId>
|
||||
<artifactId>external-example</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<version>1.0-SNAPSHOT</version>
|
||||
<name>external-example</name>
|
||||
|
||||
<properties>
|
||||
<sting.version>2.6-SNAPSHOT</sting.version>
|
||||
<!--
|
||||
sting.basedir property must point to your checkout of Sting/GATK until we can get all the
|
||||
dependencies out of the committed sting repo and into central.
|
||||
The installed pom for sting-root looks for this property.
|
||||
Alternatively, one can install all the sting files into their local ~/.m2/repository repo.
|
||||
http://maven.apache.org/plugins/maven-install-plugin/examples/custom-pom-installation.html
|
||||
-->
|
||||
<sting.basedir>../..</sting.basedir>
|
||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
|
||||
<maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
|
||||
</properties>
|
||||
|
||||
<repositories>
|
||||
<repository>
|
||||
<id>sting.public.repo.local</id>
|
||||
<name>Sting Public Local Repository</name>
|
||||
<url>file:${sting.basedir}/public/repo</url>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${sting.version}</version>
|
||||
</dependency>
|
||||
|
||||
<!--
|
||||
Test dependencies are not transitive,
|
||||
so must include each explicit test artifact.
|
||||
-->
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-utils</artifactId>
|
||||
<version>${sting.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${sting.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<version>6.8</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
|
||||
<!-- Copy test resources to your classes directory -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<version>2.8</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>unpack</id>
|
||||
<phase>process-resources</phase>
|
||||
<goals>
|
||||
<goal>unpack</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<artifactItems>
|
||||
<artifactItem>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${sting.version}</version>
|
||||
<classifier>example-resources</classifier>
|
||||
<type>tar.bz2</type>
|
||||
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
|
||||
</artifactItem>
|
||||
</artifactItems>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<!-- Generate help text -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<version>2.9.1</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>extract-resource-bundle</id>
|
||||
<goals>
|
||||
<goal>javadoc</goal>
|
||||
</goals>
|
||||
<phase>prepare-package</phase>
|
||||
<configuration>
|
||||
<doclet>org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet</doclet>
|
||||
<!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
|
||||
<docletPath>${project.build.outputDirectory}</docletPath>
|
||||
<docletArtifact>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<!-- TODO: THIS IS SUPPOSED TO BE STING-UTILS! -->
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${sting.version}</version>
|
||||
</docletArtifact>
|
||||
<maxmemory>2g</maxmemory>
|
||||
<useStandardDocletOptions>false</useStandardDocletOptions>
|
||||
<quiet>true</quiet>
|
||||
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/StingText.properties</additionalparam>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<!-- Create packaged jar, containing only your walker and required classes -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-shade-plugin</artifactId>
|
||||
<version>2.1</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<phase>package</phase>
|
||||
<goals>
|
||||
<goal>shade</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<minimizeJar>true</minimizeJar>
|
||||
<!-- Explicitly include classes loaded via reflection from artifacts below -->
|
||||
<filters>
|
||||
<filter>
|
||||
<artifact>commons-logging:commons-logging</artifact>
|
||||
<includes>
|
||||
<include>**</include>
|
||||
</includes>
|
||||
</filter>
|
||||
<filter>
|
||||
<artifact>org.broad:tribble</artifact>
|
||||
<includes>
|
||||
<include>**</include>
|
||||
</includes>
|
||||
</filter>
|
||||
<filter>
|
||||
<artifact>org.broadinstitute:variant</artifact>
|
||||
<includes>
|
||||
<include>**</include>
|
||||
</includes>
|
||||
</filter>
|
||||
</filters>
|
||||
<!-- Stop shade from trying to unzip these indirect dependencies -->
|
||||
<artifactSet>
|
||||
<excludes>
|
||||
<exclude>org.broadinstitute.sting:gsalib:tar.gz:*</exclude>
|
||||
<exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
|
||||
</excludes>
|
||||
</artifactSet>
|
||||
<transformers>
|
||||
<!-- Set the main class to the GATK -->
|
||||
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
|
||||
<mainClass>org.broadinstitute.sting.gatk.CommandLineGATK</mainClass>
|
||||
</transformer>
|
||||
<!-- Include and append to the existing gatk help text in StingText.properties -->
|
||||
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
|
||||
<resource>StingText.properties</resource>
|
||||
</transformer>
|
||||
</transformers>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<!-- surefire runs fast, small (aka unit) tests -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-surefire-plugin</artifactId>
|
||||
<version>2.16</version>
|
||||
<configuration>
|
||||
<!-- See explicit executions below -->
|
||||
<skip>true</skip>
|
||||
<systemPropertyVariables>
|
||||
<!-- TODO: Fix BaseTest to not error out if this property is missing. -->
|
||||
<pipeline.run>false</pipeline.run>
|
||||
</systemPropertyVariables>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>default-test</id>
|
||||
<phase>none</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<!-- run all non integration tests -->
|
||||
<id>unit-tests</id>
|
||||
<goals>
|
||||
<goal>test</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<skip>false</skip>
|
||||
<includes>
|
||||
<include>**/*Test.class</include>
|
||||
</includes>
|
||||
<excludes>
|
||||
<exclude>**/*IntegrationTest.class</exclude>
|
||||
</excludes>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<!-- failsafe runs all other tests that may take longer, and may require pre/post test setup and teardown -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-failsafe-plugin</artifactId>
|
||||
<version>2.16</version>
|
||||
<configuration>
|
||||
<!-- See explicit executions below -->
|
||||
<skip>true</skip>
|
||||
<systemPropertyVariables>
|
||||
<!-- TODO: Fix BaseTest to not error out if this property is missing. -->
|
||||
<pipeline.run>false</pipeline.run>
|
||||
</systemPropertyVariables>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>integration-tests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run integration tests -->
|
||||
<configuration>
|
||||
<skip>false</skip>
|
||||
<includes>
|
||||
<include>**/*IntegrationTest.class</include>
|
||||
</includes>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>GATK Framework</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>sting-utils</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>sting-utils</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.caliper</groupId>
|
||||
<artifactId>caliper</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>example-resources</id>
|
||||
<phase>generate-resources</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-resource-bundle-log4j</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>extract-resource-bundle</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<goals>
|
||||
<goal>test-jar</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-invoker-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>package-unittests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-integrationtests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-largescaletests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-pipelinetests</id>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>private</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- TODO: All tests require access to private. For now. -->
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-private-testdata</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-testdata</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,155 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>gatk-package</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>GATK Package</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<sting.unpack.phase>prepare-package</sting.unpack.phase>
|
||||
<sting.shade.phase>package</sting.shade.phase>
|
||||
<app.main.class>org.broadinstitute.sting.gatk.CommandLineGATK</app.main.class>
|
||||
<sting.binary-dist.name>GenomeAnalysisTK</sting.binary-dist.name>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<!-- Package everything in org.broadinstitute.sting -->
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<!-- Tribble codecs -->
|
||||
<dependency>
|
||||
<groupId>org.broad</groupId>
|
||||
<artifactId>tribble</artifactId>
|
||||
</dependency>
|
||||
<!-- The variant package (VCF, BCF, and VariantContext) -->
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute</groupId>
|
||||
<artifactId>variant</artifactId>
|
||||
</dependency>
|
||||
<!-- Workaround - depend on the logger impl required by JEXL -->
|
||||
<dependency>
|
||||
<groupId>commons-logging</groupId>
|
||||
<artifactId>commons-logging</artifactId>
|
||||
</dependency>
|
||||
<!-- Required for binary-dist assembly, excluded by shade -->
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<classifier>example-resources</classifier>
|
||||
<type>tar.bz2</type>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>unpack-direct-dependencies</id>
|
||||
<phase>${sting.unpack.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-shade-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>sting-executable</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>binary-dist</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-git-release</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-install-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>default-install</id>
|
||||
<phase>none</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>install-package</id>
|
||||
<phase>install</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>protected</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-protected</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</profile>
|
||||
<profile>
|
||||
<id>private</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-private</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>gatk-queue-extgen</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>Queue GATK ExtGen</name>
|
||||
<description>Queue GATK Extensions Generator</description>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>gsalib</artifactId>
|
||||
<packaging>pom</packaging>
|
||||
<name>Sting GSALib</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
|
||||
<gsalib.filename>gsalib.tar.gz</gsalib.filename>
|
||||
</properties>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>gsalib-assembly</id>
|
||||
<goals>
|
||||
<goal>single</goal>
|
||||
</goals>
|
||||
<phase>generate-resources</phase>
|
||||
<configuration>
|
||||
<appendAssemblyId>false</appendAssemblyId>
|
||||
<descriptors>
|
||||
<descriptor>src/assembly/gsalib.xml</descriptor>
|
||||
</descriptors>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,158 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-root</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../sting-root</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>sting-package-tests</artifactId>
|
||||
<packaging>pom</packaging>
|
||||
<name>Sting Package Tests</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
</properties>
|
||||
|
||||
<!-- Dependency configuration (versions, etc.) -->
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>${sting.packagetests.artifactId}</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
|
||||
<!--
|
||||
For com.sun.javadoc
|
||||
See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
|
||||
-->
|
||||
<dependency>
|
||||
<groupId>com.sun</groupId>
|
||||
<artifactId>tools</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.google.code.cofoja</groupId>
|
||||
<artifactId>cofoja</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.google.caliper</groupId>
|
||||
<artifactId>caliper</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<directory>${sting.packagetests.basedir}/target</directory>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>unittests</id>
|
||||
<build>
|
||||
<!-- Plugin configuration -->
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-surefire-plugin</artifactId>
|
||||
<configuration>
|
||||
<basedir>${sting.packagetests.basedir}</basedir>
|
||||
<workingDirectory>${sting.packagetests.basedir}</workingDirectory>
|
||||
<classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
|
||||
<testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
|
||||
<dependenciesToScan>
|
||||
<scan>org.broadinstitute.sting:.*</scan>
|
||||
</dependenciesToScan>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<!-- run all non integration tests -->
|
||||
<id>unit-tests</id>
|
||||
<goals>
|
||||
<goal>test</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<skip>${sting.packageunittests.skipped}</skip>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
|
||||
<profile>
|
||||
<id>integrationtests</id>
|
||||
<build>
|
||||
<!-- Plugin configuration -->
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-failsafe-plugin</artifactId>
|
||||
<configuration>
|
||||
<basedir>${sting.packagetests.basedir}</basedir>
|
||||
<workingDirectory>${sting.packagetests.basedir}</workingDirectory>
|
||||
<classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
|
||||
<testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
|
||||
<dependenciesToScan>
|
||||
<scan>org.broadinstitute.sting:.*</scan>
|
||||
</dependenciesToScan>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>integration-tests</id>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run integration tests -->
|
||||
<configuration>
|
||||
<skip>${sting.packageintegrationtests.skipped}</skip>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>pipeline-tests</id>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run pipeline dry run tests -->
|
||||
<configuration>
|
||||
<skip>${sting.packagepipelinetests.skipped}</skip>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>large-scale-tests</id>
|
||||
<goals>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run large scale tests -->
|
||||
<configuration>
|
||||
<skip>${sting.packagelargescaletests.skipped}</skip>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-root</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>sting-root</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>sting-public</artifactId>
|
||||
<packaging>pom</packaging>
|
||||
<name>Sting Public</name>
|
||||
|
||||
<modules>
|
||||
<module>sting-root</module>
|
||||
<module>gsalib</module>
|
||||
<module>sting-utils</module>
|
||||
<module>gatk-framework</module>
|
||||
<module>gatk-package</module>
|
||||
<!-- queue optionally enabled as profiles -->
|
||||
</modules>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/..</sting.basedir>
|
||||
</properties>
|
||||
|
||||
<profiles>
|
||||
<!-- Allow queue to be disabled. -->
|
||||
<profile>
|
||||
<id>queue</id>
|
||||
<activation>
|
||||
<property>
|
||||
<name>!disable.queue</name>
|
||||
</property>
|
||||
</activation>
|
||||
<modules>
|
||||
<module>gatk-queue-extgen</module>
|
||||
<module>queue-framework</module>
|
||||
<module>queue-package</module>
|
||||
</modules>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,267 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>queue-framework</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>Queue Framework</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
|
||||
<sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
|
||||
<sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.scala-lang</groupId>
|
||||
<artifactId>scala-compiler</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>log4j</groupId>
|
||||
<artifactId>log4j</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf.jgrapht</groupId>
|
||||
<artifactId>jgrapht</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-email</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>javax.mail</groupId>
|
||||
<artifactId>mail</artifactId>
|
||||
</dependency>
|
||||
<!--
|
||||
extgen dependency only applies to the exec:exec,
|
||||
not the artifact, but don't know another way to include
|
||||
the artifact *only* in the <classpath/> of exec.
|
||||
See https://jira.codehaus.org/browse/MEXEC-111
|
||||
|
||||
Perhaps extgen should be wrapped in a maven plugin?
|
||||
-->
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-queue-extgen</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<scope>runtime</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.codehaus.mojo</groupId>
|
||||
<artifactId>exec-maven-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>generate-gatk-extensions</id>
|
||||
<goals>
|
||||
<goal>exec</goal>
|
||||
</goals>
|
||||
<phase>generate-sources</phase>
|
||||
<configuration>
|
||||
<skip>${sting.generate-gatk-extensions.skipped}</skip>
|
||||
<executable>java</executable>
|
||||
<arguments>
|
||||
<argument>-classpath</argument>
|
||||
<classpath />
|
||||
<argument>org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator</argument>
|
||||
<argument>-l</argument>
|
||||
<argument>WARN</argument>
|
||||
<argument>-outDir</argument>
|
||||
<argument>${gatk.extensions.sources}</argument>
|
||||
</arguments>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.codehaus.mojo</groupId>
|
||||
<artifactId>build-helper-maven-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>add-gatk-extensions</id>
|
||||
<goals>
|
||||
<goal>add-source</goal>
|
||||
</goals>
|
||||
<phase>generate-sources</phase>
|
||||
<configuration>
|
||||
<sources>
|
||||
<source>${gatk.extensions.sources}</source>
|
||||
</sources>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>example-resources</id>
|
||||
<phase>generate-resources</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.scala-tools</groupId>
|
||||
<artifactId>maven-scala-plugin</artifactId>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-public-qscript</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-public-qscript</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-resource-bundle-log4j</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>extract-resource-bundle</id>
|
||||
<phase>prepare-package</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<goals>
|
||||
<goal>test-jar</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-invoker-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>package-unittests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-integrationtests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-largescaletests</id>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>package-pipelinetests</id>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>protected</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-protected</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</profile>
|
||||
<profile>
|
||||
<id>private</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-private</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- TODO: All tests require access to private. For now. -->
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-private-testdata</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-testdata</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>link-private-qscript</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-qscript</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,170 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>queue-package</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>Queue Package</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<sting.unpack.phase>prepare-package</sting.unpack.phase>
|
||||
<sting.shade.phase>package</sting.shade.phase>
|
||||
<sting.binary-dist.name>Queue</sting.binary-dist.name>
|
||||
<app.main.class>org.broadinstitute.sting.queue.QCommandLine</app.main.class>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<!-- Queue -->
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>queue-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-package</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<!-- Scala -->
|
||||
<dependency>
|
||||
<groupId>org.scala-lang</groupId>
|
||||
<artifactId>scala-library</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.scala-lang</groupId>
|
||||
<artifactId>scala-compiler</artifactId>
|
||||
</dependency>
|
||||
<!-- Picard -->
|
||||
<dependency>
|
||||
<groupId>net.sf</groupId>
|
||||
<artifactId>picard</artifactId>
|
||||
</dependency>
|
||||
<!-- JavaMail -->
|
||||
<dependency>
|
||||
<groupId>javax.mail</groupId>
|
||||
<artifactId>mail</artifactId>
|
||||
</dependency>
|
||||
<!-- JNA, including embedded native libraries -->
|
||||
<dependency>
|
||||
<groupId>net.java.dev.jna</groupId>
|
||||
<artifactId>jna</artifactId>
|
||||
</dependency>
|
||||
<!-- Contracts for Java -->
|
||||
<dependency>
|
||||
<groupId>com.google.code.cofoja</groupId>
|
||||
<artifactId>cofoja</artifactId>
|
||||
</dependency>
|
||||
<!-- snpEff -->
|
||||
<dependency>
|
||||
<groupId>net.sf.snpeff</groupId>
|
||||
<artifactId>snpeff</artifactId>
|
||||
</dependency>
|
||||
<!-- Required for binary-dist assembly, excluded by shade -->
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gatk-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<classifier>example-resources</classifier>
|
||||
<type>tar.bz2</type>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>queue-framework</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<classifier>example-resources</classifier>
|
||||
<type>tar.bz2</type>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>unpack-direct-dependencies</id>
|
||||
<phase>${sting.unpack.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-shade-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>sting-executable</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>binary-dist</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-git-release</id>
|
||||
<phase>${sting.shade.phase}</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-install-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>default-install</id>
|
||||
<phase>none</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>install-package</id>
|
||||
<phase>install</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<profiles>
|
||||
<profile>
|
||||
<id>private</id>
|
||||
<activation>
|
||||
<file>
|
||||
<exists>${basedir}/../../private/queue-private/pom.xml</exists>
|
||||
</file>
|
||||
</activation>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>queue-private</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,619 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<!--
|
||||
This pom is parent for all sting/gatk poms
|
||||
See also:
|
||||
http://maven.apache.org/pom.html#Inheritance_v
|
||||
http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
|
||||
http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
|
||||
-->
|
||||
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-root</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<packaging>pom</packaging>
|
||||
<name>Sting Root</name>
|
||||
|
||||
<prerequisites>
|
||||
<maven>3.0.4</maven>
|
||||
</prerequisites>
|
||||
|
||||
<properties>
|
||||
<sourceEncoding>UTF-8</sourceEncoding>
|
||||
<project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
|
||||
<project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
|
||||
<maven.compiler.source>1.7</maven.compiler.source>
|
||||
<maven.compiler.target>1.7</maven.compiler.target>
|
||||
<maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<sting.committests.skipped>true</sting.committests.skipped>
|
||||
<sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
|
||||
<sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
|
||||
<sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped>
|
||||
<sting.largescaletests.skipped>true</sting.largescaletests.skipped>
|
||||
<sting.pipelinetests.run>false</sting.pipelinetests.run>
|
||||
<test.maxmemory>4g</test.maxmemory>
|
||||
<test.args>-Xmx${test.maxmemory}</test.args>
|
||||
</properties>
|
||||
|
||||
<!-- Dependency configuration (versions, etc.) -->
|
||||
<dependencyManagement>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.scala-lang</groupId>
|
||||
<artifactId>scala-compiler</artifactId>
|
||||
<version>2.10.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.scala-lang</groupId>
|
||||
<artifactId>scala-library</artifactId>
|
||||
<version>2.10.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.code.cofoja</groupId>
|
||||
<artifactId>cofoja</artifactId>
|
||||
<version>1.0-r139</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf</groupId>
|
||||
<artifactId>sam</artifactId>
|
||||
<version>1.104.1628</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf</groupId>
|
||||
<artifactId>picard</artifactId>
|
||||
<version>1.104.1628</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>edu.mit.broad</groupId>
|
||||
<artifactId>picard-private-parts</artifactId>
|
||||
<version>2872</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.broad</groupId>
|
||||
<artifactId>tribble</artifactId>
|
||||
<version>1.104.1628</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute</groupId>
|
||||
<artifactId>variant</artifactId>
|
||||
<version>1.105.1642</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>log4j</groupId>
|
||||
<artifactId>log4j</artifactId>
|
||||
<version>1.2.15</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.sun.jdmk</groupId>
|
||||
<artifactId>jmxtools</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>javax.jms</groupId>
|
||||
<artifactId>jms</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>com.sun.jmx</groupId>
|
||||
<artifactId>jmxri</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>javax.mail</groupId>
|
||||
<artifactId>mail</artifactId>
|
||||
<version>1.4.4</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>colt</groupId>
|
||||
<artifactId>colt</artifactId>
|
||||
<version>1.2.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>it.unimi.dsi</groupId>
|
||||
<artifactId>fastutil</artifactId>
|
||||
<version>6.5.3</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.simpleframework</groupId>
|
||||
<artifactId>simple-xml</artifactId>
|
||||
<version>2.0.4</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.bcel</groupId>
|
||||
<artifactId>bcel</artifactId>
|
||||
<version>5.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.reflections</groupId>
|
||||
<artifactId>reflections</artifactId>
|
||||
<version>0.9.8</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.slf4j</groupId>
|
||||
<artifactId>slf4j-log4j12</artifactId>
|
||||
<version>1.6.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>gov.nist</groupId>
|
||||
<artifactId>Jama</artifactId>
|
||||
<version>1.0.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf.jgrapht</groupId>
|
||||
<artifactId>jgrapht</artifactId>
|
||||
<version>0.8.3</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.freemarker</groupId>
|
||||
<artifactId>freemarker</artifactId>
|
||||
<version>2.3.18</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-email</artifactId>
|
||||
<version>1.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-jexl</artifactId>
|
||||
<version>2.1.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-lang</groupId>
|
||||
<artifactId>commons-lang</artifactId>
|
||||
<version>2.5</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-logging</groupId>
|
||||
<artifactId>commons-logging</artifactId>
|
||||
<version>1.1.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-io</groupId>
|
||||
<artifactId>commons-io</artifactId>
|
||||
<version>2.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-collections</groupId>
|
||||
<artifactId>commons-collections</artifactId>
|
||||
<version>3.2.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-math</artifactId>
|
||||
<version>2.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.java.dev.jna</groupId>
|
||||
<artifactId>jna</artifactId>
|
||||
<version>3.2.7</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.java.dev.jets3t</groupId>
|
||||
<artifactId>jets3t</artifactId>
|
||||
<version>0.8.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf.gridscheduler</groupId>
|
||||
<artifactId>drmaa</artifactId>
|
||||
<version>6.2u5p2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.uncommons</groupId>
|
||||
<artifactId>reportng</artifactId>
|
||||
<version>1.1.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.inject</groupId>
|
||||
<artifactId>guice</artifactId>
|
||||
<version>3.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.poi</groupId>
|
||||
<artifactId>poi</artifactId>
|
||||
<version>3.8-beta3</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.poi</groupId>
|
||||
<artifactId>poi-ooxml</artifactId>
|
||||
<version>3.8-beta3</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf.snpeff</groupId>
|
||||
<artifactId>snpeff</artifactId>
|
||||
<version>2.0.5</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.mongodb</groupId>
|
||||
<artifactId>mongo-java-driver</artifactId>
|
||||
<version>2.7.3</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.code.gson</groupId>
|
||||
<artifactId>gson</artifactId>
|
||||
<version>2.2.2</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.httpcomponents</groupId>
|
||||
<artifactId>httpclient</artifactId>
|
||||
<version>4.1.1</version>
|
||||
</dependency>
|
||||
|
||||
<!--
|
||||
For com.sun.javadoc
|
||||
See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
|
||||
-->
|
||||
<dependency>
|
||||
<groupId>com.sun</groupId>
|
||||
<artifactId>tools</artifactId>
|
||||
<version>1.4.2</version>
|
||||
<scope>system</scope>
|
||||
<systemPath>${java.home}/../lib/tools.jar</systemPath>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<version>6.8</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.caliper</groupId>
|
||||
<artifactId>caliper</artifactId>
|
||||
<version>0.5-rc1</version>
|
||||
<scope>test</scope>
|
||||
<exclusions>
|
||||
<!--
|
||||
TODO: After upgrade to caliper 1.0-beta-1 or later, this may need a revisit.
|
||||
Possibly other modules may need to exclude *their* old guava versions.
|
||||
-->
|
||||
<exclusion>
|
||||
<groupId>com.google.guava</groupId>
|
||||
<artifactId>guava</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</dependencyManagement>
|
||||
|
||||
<build>
|
||||
<!-- Plugin configuration -->
|
||||
<pluginManagement>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.codehaus.mojo</groupId>
|
||||
<artifactId>exec-maven-plugin</artifactId>
|
||||
<version>1.2.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>com.lukegb.mojo</groupId>
|
||||
<artifactId>gitdescribe-maven-plugin</artifactId>
|
||||
<version>2.0</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.codehaus.mojo</groupId>
|
||||
<artifactId>build-helper-maven-plugin</artifactId>
|
||||
<version>1.8</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-clean-plugin</artifactId>
|
||||
<version>2.5</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<version>2.8</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<version>2.6</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<version>2.9.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.scala-tools</groupId>
|
||||
<artifactId>maven-scala-plugin</artifactId>
|
||||
<version>2.15.2</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<version>2.4</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-shade-plugin</artifactId>
|
||||
<version>2.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<version>2.4</version>
|
||||
</plugin>
|
||||
|
||||
<!--
|
||||
surefire/failsafe configurations are global, even across poms
|
||||
not directly aggregated, for example package-tests/pom.xml
|
||||
-->
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-surefire-plugin</artifactId>
|
||||
<version>2.16</version>
|
||||
<configuration>
|
||||
<!-- See explicit executions below -->
|
||||
<skip>true</skip>
|
||||
<failIfNoTests>false</failIfNoTests>
|
||||
<useFile>false</useFile>
|
||||
<reportFormat>plain</reportFormat>
|
||||
<argLine>${test.args}</argLine>
|
||||
<properties>
|
||||
<property>
|
||||
<name>usedefaultlisteners</name>
|
||||
<value>false</value>
|
||||
<!-- TODO: Why do the default listeners take so long post tests, what is the "old" directory, and why doesn't ant have this problem? -->
|
||||
</property>
|
||||
</properties>
|
||||
<systemPropertyVariables>
|
||||
<clover.pertest.coverage>diff</clover.pertest.coverage>
|
||||
<java.awt.headless>true</java.awt.headless>
|
||||
<!-- TODO: Fix BaseTest to not error out if this property is missing. -->
|
||||
<pipeline.run>${sting.pipelinetests.run}</pipeline.run>
|
||||
<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
|
||||
</systemPropertyVariables>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>default-test</id>
|
||||
<phase>none</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<!-- run all non integration tests -->
|
||||
<id>unit-tests</id>
|
||||
<goals>
|
||||
<goal>test</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<!-- TODO: Re-enable unit tests by default? -->
|
||||
<skip>${sting.unittests.skipped}</skip>
|
||||
<includes>
|
||||
<include>**/*Test.class</include>
|
||||
</includes>
|
||||
<excludes>
|
||||
<exclude>**/*IntegrationTest.class</exclude>
|
||||
<exclude>**/*PipelineTest.class</exclude>
|
||||
<exclude>**/*LargeScaleTest.class</exclude>
|
||||
</excludes>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-failsafe-plugin</artifactId>
|
||||
<version>2.16</version>
|
||||
<configuration>
|
||||
<!-- See explicit executions below -->
|
||||
<skip>true</skip>
|
||||
<failIfNoTests>false</failIfNoTests>
|
||||
<useFile>false</useFile>
|
||||
<reportFormat>plain</reportFormat>
|
||||
<argLine>${test.args}</argLine>
|
||||
<properties>
|
||||
<property>
|
||||
<name>usedefaultlisteners</name>
|
||||
<value>false</value>
|
||||
<!-- TODO: Why do the default listeners take so long post tests, what is the "old" directory, and why doesn't ant have this problem? -->
|
||||
</property>
|
||||
</properties>
|
||||
<systemPropertyVariables>
|
||||
<clover.pertest.coverage>diff</clover.pertest.coverage>
|
||||
<java.awt.headless>true</java.awt.headless>
|
||||
<!-- TODO: Fix BaseTest to not error out if this property is missing. -->
|
||||
<pipeline.run>${sting.pipelinetests.run}</pipeline.run>
|
||||
<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
|
||||
</systemPropertyVariables>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>integration-tests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run integration tests -->
|
||||
<configuration>
|
||||
<!-- TODO: Re-enable integration tests by default? -->
|
||||
<skip>${sting.integrationtests.skipped}</skip>
|
||||
<includes>
|
||||
<include>**/*IntegrationTest.class</include>
|
||||
</includes>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>pipeline-tests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run pipeline dry run tests -->
|
||||
<configuration>
|
||||
<!-- TODO: Re-enable pipeline tests by default? -->
|
||||
<skip>${sting.pipelinetests.skipped}</skip>
|
||||
<includes>
|
||||
<include>**/*PipelineTest.class</include>
|
||||
</includes>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>large-scale-tests</id>
|
||||
<goals>
|
||||
<goal>integration-test</goal>
|
||||
<goal>verify</goal>
|
||||
</goals>
|
||||
<!-- run large scale tests -->
|
||||
<configuration>
|
||||
<skip>${sting.largescaletests.skipped}</skip>
|
||||
<includes>
|
||||
<include>**/*LargeScaleTest.class</include>
|
||||
</includes>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
||||
<plugin>
|
||||
<groupId>com.google.code.sortpom</groupId>
|
||||
<artifactId>maven-sortpom-plugin</artifactId>
|
||||
<version>2.2</version>
|
||||
<configuration>
|
||||
<createBackupFile>false</createBackupFile>
|
||||
<predefinedSortOrder>custom_1</predefinedSortOrder>
|
||||
<lineSeparator>\n</lineSeparator>
|
||||
<encoding>${sourceEncoding}</encoding>
|
||||
<keepBlankLines>true</keepBlankLines>
|
||||
<sortDependencies>scope</sortDependencies>
|
||||
<nrOfIndentSpace>4</nrOfIndentSpace>
|
||||
<expandEmptyElements>false</expandEmptyElements>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<goals>
|
||||
<goal>sort</goal>
|
||||
</goals>
|
||||
<phase>verify</phase>
|
||||
</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>
|
||||
<version>1.0.3</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-invoker-plugin</artifactId>
|
||||
<version>1.8</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-install-plugin</artifactId>
|
||||
<version>2.5</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-site-plugin</artifactId>
|
||||
<version>3.3</version>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</pluginManagement>
|
||||
|
||||
<!-- Invoke plugins that always run -->
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>com.lukegb.mojo</groupId>
|
||||
<artifactId>gitdescribe-maven-plugin</artifactId>
|
||||
<configuration>
|
||||
<extraArguments>
|
||||
<param>--long</param>
|
||||
</extraArguments>
|
||||
<setReactorProjectsProperties>true</setReactorProjectsProperties>
|
||||
<descriptionProperty>git.version</descriptionProperty>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>gitdescribe-initialize</id>
|
||||
<goals>
|
||||
<goal>gitdescribe</goal>
|
||||
</goals>
|
||||
<phase>initialize</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>gitdescribe-presite</id>
|
||||
<goals>
|
||||
<goal>gitdescribe</goal>
|
||||
</goals>
|
||||
<phase>pre-site</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.codehaus.mojo</groupId>
|
||||
<artifactId>build-helper-maven-plugin</artifactId>
|
||||
<!-- TODO: gitdescribe plugin doesn't allow null prefixes -->
|
||||
<executions>
|
||||
<execution>
|
||||
<id>fix-version-initialize</id>
|
||||
<goals>
|
||||
<goal>regex-property</goal>
|
||||
</goals>
|
||||
<phase>initialize</phase>
|
||||
<configuration>
|
||||
<name>build.version</name>
|
||||
<value>${git.version}</value>
|
||||
<regex>git-</regex>
|
||||
</configuration>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>fix-version-pre-site</id>
|
||||
<goals>
|
||||
<goal>regex-property</goal>
|
||||
</goals>
|
||||
<phase>pre-site</phase>
|
||||
<configuration>
|
||||
<name>build.version</name>
|
||||
<value>${git.version}</value>
|
||||
<regex>git-</regex>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>com.google.code.sortpom</groupId>
|
||||
<artifactId>maven-sortpom-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>default</id>
|
||||
<goals>
|
||||
<goal>sort</goal>
|
||||
</goals>
|
||||
<phase>verify</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<reporting>
|
||||
<excludeDefaults>true</excludeDefaults>
|
||||
</reporting>
|
||||
|
||||
<repositories>
|
||||
<repository>
|
||||
<id>sting.public.repo.local</id>
|
||||
<name>Sting Public Local Repository</name>
|
||||
<url>file:${sting.basedir}/public/repo</url>
|
||||
</repository>
|
||||
<repository>
|
||||
<id>sting.private.repo.local</id>
|
||||
<name>Sting Private Local Repository</name>
|
||||
<url>file:${sting.basedir}/private/repo</url>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,170 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.broadinstitute.sting</groupId>
|
||||
<artifactId>sting-aggregator</artifactId>
|
||||
<version>2.6-SNAPSHOT</version>
|
||||
<relativePath>../..</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>sting-utils</artifactId>
|
||||
<packaging>jar</packaging>
|
||||
<name>Sting Utils</name>
|
||||
|
||||
<properties>
|
||||
<sting.basedir>${project.basedir}/../..</sting.basedir>
|
||||
<gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
|
||||
<gsalib.filename>gsalib.tar.gz</gsalib.filename>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>net.sf</groupId>
|
||||
<artifactId>sam</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf</groupId>
|
||||
<artifactId>picard</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.broad</groupId>
|
||||
<artifactId>tribble</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.broadinstitute</groupId>
|
||||
<artifactId>variant</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>log4j</groupId>
|
||||
<artifactId>log4j</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>colt</groupId>
|
||||
<artifactId>colt</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>it.unimi.dsi</groupId>
|
||||
<artifactId>fastutil</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.simpleframework</groupId>
|
||||
<artifactId>simple-xml</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.reflections</groupId>
|
||||
<artifactId>reflections</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.slf4j</groupId>
|
||||
<artifactId>slf4j-log4j12</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.freemarker</groupId>
|
||||
<artifactId>freemarker</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-jexl</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-lang</groupId>
|
||||
<artifactId>commons-lang</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-io</groupId>
|
||||
<artifactId>commons-io</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>commons-collections</groupId>
|
||||
<artifactId>commons-collections</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-math</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.java.dev.jna</groupId>
|
||||
<artifactId>jna</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.java.dev.jets3t</groupId>
|
||||
<artifactId>jets3t</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>net.sf.gridscheduler</groupId>
|
||||
<artifactId>drmaa</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.code.gson</groupId>
|
||||
<artifactId>gson</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.httpcomponents</groupId>
|
||||
<artifactId>httpclient</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.code.cofoja</groupId>
|
||||
<artifactId>cofoja</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gsalib</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>tar.gz</type>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.testng</groupId>
|
||||
<artifactId>testng</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.caliper</groupId>
|
||||
<artifactId>caliper</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-gsalib</id>
|
||||
<goals>
|
||||
<goal>copy</goal>
|
||||
</goals>
|
||||
<phase>process-resources</phase>
|
||||
<configuration>
|
||||
<artifactItems>
|
||||
<artifactItem>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>gsalib</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>tar.gz</type>
|
||||
<outputDirectory>${project.build.outputDirectory}/${gsalib.packagedir}</outputDirectory>
|
||||
<destFileName>${gsalib.filename}</destFileName>
|
||||
</artifactItem>
|
||||
</artifactItems>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<goals>
|
||||
<goal>test-jar</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
Loading…
Reference in New Issue