pom.xml

<?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/xsd/maven-4.0.0.xsd">

  <parent>
    <groupId>org.sonatype.oss</groupId>
    <artifactId>oss-parent</artifactId>
    <version>7</version>
    <relativePath/>
  </parent>
  
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.bdgenomics.xASSEMBLEx</groupId>
  <artifactId>xASSEMBLEx-parent</artifactId>
  <version>0.0.1</version>
  <packaging>pom</packaging>
  <name>xASSEMBLEx: an ADAM/GraphX based assembler</name>

  <properties>
    <adam.version>0.12.1-SNAPSHOT</adam.version>
    <avro.version>1.7.4</avro.version>
    <java.version>1.7</java.version>
    <scala.version>2.10.3</scala.version>
    <scala.version.prefix>2.10</scala.version.prefix>
    <spark.version>1.0.0</spark.version>
    <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
    <hadoop.version>2.2.0</hadoop.version>
  </properties>

  <modules>
    <module>xASSEMBLEx-core</module>
    <module>xASSEMBLEx-cli</module>
  </modules>

  <licenses>
    <license>
      <name>Apache License</name>
      <url>https://raw.github.com/fnothaft/xASSEMBLEx/master/LICENSE.txt</url>
      <distribution>repo</distribution>
    </license>
  </licenses>

  <scm>
    <connection>scm:git:git@github.com:fnothaft/xASSEMBLEx.git</connection>
    <developerConnection>scm:git:git@github.com:fnothaft/xASSEMBLEx.git</developerConnection>
    <url>scm:git:git@github.com:fnothaft/xASSEMBLEx.git</url>
    <tag>HEAD</tag>
  </scm>

  <developers>
    <developer>
      <id>fnothaft</id>
      <name>Frank Austin Nothaft</name>
      <email>fnothaft@berkeley.edu</email>
      <url>http://www.fnothaft.net</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
  </developers>

  <issueManagement>
    <system>github</system>
    <url>https://github.com/fnothaft/xASSEMBLEx/issues</url>
  </issueManagement>

  <build>
    <outputDirectory>target/scala-${scala.version}/classes</outputDirectory>
    <testOutputDirectory>target/scala-${scala.version}/test-classes</testOutputDirectory>
    <plugins>
      <plugin>
        <groupId>com.mycila.maven-license-plugin</groupId>
        <artifactId>maven-license-plugin</artifactId>
        <version>1.10.b1</version>
        <configuration>
          <header>LICENSE_header.txt</header>
          <strictCheck>true</strictCheck>
          <properties>
            <owner>Big Data Genomics Developers</owner>
            <email>adam-developers@googlegroups.com</email>
          </properties>
          <includes>
            <include>**/src/main/scala/**</include>
            <include>**/src/test/scala/**</include>
            <include>**/src/main/java/**</include>
            <include>**/src/test/scala/**</include>
          </includes>
        </configuration>
        <executions>
          <execution>
            <goals>
              <goal>check</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.1</version>
        <configuration>
          <source>${java.version}</source>
          <target>${java.version}</target>
        </configuration>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
        <version>3.1.5</version>
        <executions>
          <execution>
            <id>scala-compile-first</id>
            <phase>process-resources</phase>
            <goals>
              <goal>compile</goal>
            </goals>
          </execution>
          <execution>
            <id>scala-test-compile-first</id>
            <phase>process-test-resources</phase>
            <goals>
              <goal>testCompile</goal>
            </goals>
          </execution>
          <execution>
            <id>attach-scaladocs</id>
            <phase>verify</phase>
            <goals>
              <goal>doc-jar</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <scalaVersion>${scala.version}</scalaVersion>
          <recompileMode>incremental</recompileMode>
          <useZincServer>true</useZincServer>
          <args>
            <arg>-unchecked</arg>
            <arg>-optimise</arg>
            <arg>-deprecation</arg>
          </args>
          <jvmArgs>
            <jvmArg>-Xms64m</jvmArg>
            <jvmArg>-Xms1024m</jvmArg>
            <jvmArg>-Xmx1024m</jvmArg>
          </jvmArgs>
          <javacArgs>
            <javacArg>-source</javacArg>
            <javacArg>${java.version}</javacArg>
            <javacArg>-target</javacArg>
            <javacArg>${java.version}</javacArg>
          </javacArgs>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-shade-plugin</artifactId>
        <version>2.1</version>
      </plugin>
      <!-- disable surefire -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>2.7</version>
        <configuration>
          <skipTests>true</skipTests>
        </configuration>
      </plugin>
      <!-- enable scalatest -->
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
        <version>1.0-RC2</version>
      </plugin>
      <plugin>
        <groupId>org.scalariform</groupId>
        <artifactId>scalariform-maven-plugin</artifactId>
        <version>0.1.4</version>
        <executions>
          <execution>
            <phase>process-sources</phase>
            <goals>
              <goal>format</goal>
            </goals>
            <configuration>
              <alignParameters>true</alignParameters>
              <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
              <doubleIndentClassDeclaration>true</doubleIndentClassDeclaration>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>

  <repositories>
    <repository>
      <id>Sonatype</id>
      <url>http://oss.sonatype.org/content/repositories/snapshots/</url>
    </repository>
    <repository>
      <id>Apache</id>
      <url>http://people.apache.org/repo/m2-snapshot-repository</url>
    </repository>
  </repositories>

  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>org.apache.hadoop</groupId>
        <artifactId>hadoop-client</artifactId>
        <version>${hadoop.version}</version>
        <exclusions>
          <exclusion>
            <groupId>asm</groupId>
            <artifactId>asm</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.jboss.netty</groupId>
            <artifactId>netty</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.sonatype.sisu.inject</groupId>
            <artifactId>*</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.apache.hadoop</groupId>
        <artifactId>hadoop-client</artifactId>
        <version>${hadoop.version}</version>
        <exclusions>
          <exclusion>
            <groupId>asm</groupId>
            <artifactId>asm</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.jboss.netty</groupId>
            <artifactId>netty</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.sonatype.sisu.inject</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>javax.servlet</groupId>
            <artifactId>*</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-core</artifactId>
        <version>${adam.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-core</artifactId>
        <version>${adam.version}</version>
        <type>test-jar</type>
        <scope>test</scope>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-cli</artifactId>
        <version>${adam.version}</version>
      </dependency>
      <dependency>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest_${scala.version.prefix}</artifactId>
        <version>1.9.2</version>
        <scope>test</scope>
      </dependency>
      <dependency>
        <groupId>commons-configuration</groupId>
        <artifactId>commons-configuration</artifactId>
        <version>1.10</version>
      </dependency>
      <dependency>
        <groupId>args4j</groupId>
        <artifactId>args4j</artifactId>
        <version>2.0.23</version>
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-core_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-graphx_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
      </dependency>
    </dependencies>
  </dependencyManagement>
</project>