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pom.xml
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pom.xml
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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">
<modelVersion>4.0.0</modelVersion>
<!-- Properties for your assembly -->
<groupId>org.broadinstitute.cga</groupId>
<artifactId>mutect</artifactId>
<packaging>jar</packaging>
<version>1.1.7</version>
<name>Mutect</name>
<properties>
<sting.version>3.1</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>../../gatk-protected</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>
<!-- NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad. -->
<sting.committests.skipped>false</sting.committests.skipped>
<sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
<sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
<!-- This flag is used by the package tests to disable re-shading -->
<sting.shade.phase>package</sting.shade.phase>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
</properties>
<repositories>
<repository>
<id>sting.public.repo.local</id>
<name>Sting Public Local Repository</name>
<url>file:${sting.basedir}/public/repo</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>gatk-protected</artifactId>
<version>${sting.version}</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>gatk-framework</artifactId>
<version>${sting.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<!-- TODO: Move the files to conventional maven directories, instead of configuring here. -->
<sourceDirectory>${basedir}/src</sourceDirectory>
<testSourceDirectory>${basedir}/test</testSourceDirectory>
<resources>
<resource>
<directory>resources</directory>
<filtering>true</filtering>
<includes>
<include>**/MuTectText.properties</include>
</includes>
</resource>
</resources>
<plugins>
<!-- Copy test resources to your classes directory -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<executions>
<execution>
<id>unpack</id>
<phase>process-resources</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>gatk-framework</artifactId>
<version>${sting.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<!-- Create packaged jar, containing only your walker and required classes -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<executions>
<execution>
<phase>${sting.shade.phase}</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>
<filter>
<artifact>org.broadinstitute.sting:gatk-framework</artifact>
<includes>
<include>**</include>
</includes>
</filter>
<filter>
<artifact>org.broadinstitute.sting:gatk-protected</artifact>
<includes>
<include>**</include>
</includes>
</filter>
<filter>
<artifact>org.apache.commons:commons-math</artifact>
<includes>
<include>**</include>
</includes>
</filter>
<filter>
<artifact>org.broadinstitute.sting:sting-utils</artifact>
<includes>
<include>**</include>
</includes>
</filter>
<filter>
<artifact>colt:colt</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>
<plugin>
<groupId>com.lukegb.mojo</groupId>
<artifactId>gitdescribe-maven-plugin</artifactId>
<version>2.0</version>
<configuration>
<extraArguments>
<param>--long</param>
</extraArguments>
<setReactorProjectsProperties>true</setReactorProjectsProperties>
<descriptionProperty>git.version</descriptionProperty>
<failOutput>exported</failOutput>
</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>
<version>1.8</version>
<!-- 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>
</plugins>
</build>
<profiles>
<profile>
<id>packagetests-enabled</id>
<activation>
<property>
<name>sting.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<sting.shade.phase>none</sting.shade.phase>
</properties>
</profile>
</profiles>
</project>