<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>1.0</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-1.0</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>v1beta2-rev9-1.19.0</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>v1beta2-0.19</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>
  </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>
        </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>
          <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>
    </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>1.19.0</google.api.version>
    <google.api.genomics.version>v1beta2-rev7-1.19.0</google.api.genomics.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>
