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gatk-tools-java/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>
<groupId>com.google.cloud.genomics</groupId>
<artifactId>gatk-tools-java</artifactId>
<packaging>jar</packaging>
<name>Google Genomics Utils for GATK</name>
<description>Common Java files for Google Genomics integrations with GATK/Picard/HTSJDK</description>
<url>https://github.com/googlegenomics/gatk-tools-java</url>
<version>v1-0.6-SNAPSHOT</version>
<organization>
<name>Google</name>
<url>http://www.google.com/</url>
</organization>
<licenses>
<license>
<name>The Apache Software License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>iliat</id>
<name>Ilia Tulchinsky</name>
<organization>Google</organization>
<organizationUrl>http://www.google.com</organizationUrl>
<timezone>-5</timezone>
</developer>
<developer>
<id>dloy</id>
<organization>Google</organization>
<organizationUrl>http://www.google.com</organizationUrl>
<timezone>-7</timezone>
</developer>
</developers>
<scm>
<connection>scm:git:git@github.com:googlegenomics/gatk-tools-java.git</connection>
<developerConnection>scm:git:git@github.com:googlegenomics/gatk-tools-java.git</developerConnection>
<url>git@github.com:googlegenomics/gatk-tools-java.git</url>
<tag>gatk-tools-java-1.1</tag>
</scm>
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<dependencies>
<!-- Google client dependencies -->
<dependency>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
<version>${google.api.version}</version>
<exclusions>
<!-- Exclude an old version of guava which is being pulled
in by a transitive dependency google-api-client 1.19.0 -->
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava-jdk5</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client</artifactId>
<version>${google.api.version}</version>
</dependency>
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client-jetty</artifactId>
<version>${google.api.version}</version>
</dependency>
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client-java6</artifactId>
<version>${google.api.version}</version>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client</artifactId>
<version>${google.api.version}</version>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client-jackson2</artifactId>
<version>${google.api.version}</version>
</dependency>
<dependency>
<groupId>com.google.apis</groupId>
<artifactId>google-api-services-genomics</artifactId>
<version>${google.api.genomics.version}</version>
<exclusions>
<!-- Exclude an old version of guava which is being pulled
in by a transitive dependency google-api-client 1.19.0 -->
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava-jdk5</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.cloud.genomics</groupId>
<artifactId>google-genomics-utils</artifactId>
<version>v1-0.6</version>
<exclusions>
<!-- Exclude an old version of guava which is being pulled
in by a transitive dependency google-api-client 1.19.0 -->
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava-jdk5</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.128</version>
<exclusions>
<exclusion>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
</dependency>
<dependency>
<groupId>gov.nist.math.jama</groupId>
<artifactId>gov.nist.math.jama</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.9.9</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jetty</artifactId>
<version>${jetty.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jetty-util</artifactId>
<version>${jetty.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>1.10.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
<version>${jcommander.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
<version>${io.grpc.version}</version>
</dependency>
</dependencies>
<profiles>
<profile>
<id>release</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>package-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<additionalparam>-Xdoclint:none</additionalparam>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
<releaseProfiles>release</releaseProfiles>
<useReleaseProfile>false</useReleaseProfile>
<goals>deploy</goals>
</configuration>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<version>2.2.0</version>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.4.0</version>
<extensions>true</extensions>
<configuration>
<instructions>
<!-- Embed all dependencies -->
<Embed-Transitive>true</Embed-Transitive>
<Embed-Dependency>*;scope=compile|runtime;inline=true</Embed-Dependency>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>minimized</shadedClassifierName>
<minimizeJar>true</minimizeJar>
<artifactSet>
<excludes>
<exclude>com.beust:*</exclude>
<exclude>com.github.samtools:*</exclude>
<exclude>commons-logging:*</exclude>
<exclude>org.apache.maven:lib:tests</exclude>
<exclude>junit:junit</exclude>
<exclude>jmock:*</exclude>
</excludes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<properties>
<jetty.version>6.1.26</jetty.version>
<jackson.version>2.4.2</jackson.version>
<junit.version>4.11</junit.version>
<google.api.version>1.22.0</google.api.version>
<google.api.genomics.version>v1-rev87-1.22.0</google.api.genomics.version>
<io.grpc.version>0.15.0</io.grpc.version>
<mockito.version>1.10.8</mockito.version>
<jcommander.version>1.35</jcommander.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<java.version>1.7</java.version>
</properties>
</project>