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.deca</groupId>
  <artifactId>deca-parent_2.11</artifactId>
  <version>0.2.1-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>deca: Distributed Exome CNV Analyzer</name>
  
  <properties>
    <java.version>1.8</java.version>
    <adam.version>0.24.0</adam.version>
    <avro.version>1.8.0</avro.version>
    <scala.version>2.11.8</scala.version>
    <scala.version.prefix>2.11</scala.version.prefix>
    <spark.version>2.1.0</spark.version>
    <breeze.version>0.12</breeze.version>
    <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
    <hadoop.version>2.7.3</hadoop.version>
    <utils.version>0.2.13</utils.version>
    <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
  </properties>
  
  <modules>
    <module>deca-core</module>
    <module>deca-cli</module>
  </modules>

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

  <scm>
    <connection>scm:git:git@github.com:bigdatagenomics/deca.git</connection>
    <developerConnection>scm:git:git@github.com:bigdatagenomics/deca.git</developerConnection>
    <url>scm:git:git@github.com:bigdatagenomics/deca.git</url>
    <tag>HEAD</tag>
  </scm>

  <developers>
    <developer>
      <id>dchia</id>
      <name>Davin Chia</name>
      <email>dchia@middlebury.edu</email>
      <organization>Middlebury College, Department of Computer Science</organization>
      <organizationUrl>http://www.middlebury.edu/academics/cs</organizationUrl>
    </developer>
    <developer>
      <id>mlinderman</id>
      <name>Michael Linderman</name>
      <email>mlinderman@middlebury.edu</email>
      <url>http://www.cs.middlebury.edu/~mlinderman/</url>
      <organization>Middlebury College, Department of Computer Science</organization>
      <organizationUrl>http://www.middlebury.edu/academics/cs</organizationUrl>
    </developer>
    <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/bigdatagenomics/deca/issues</url>
  </issueManagement>

  <build>
    <outputDirectory>target/scala-${scala.version}/classes</outputDirectory>
    <testOutputDirectory>target/scala-${scala.version}/test-classes</testOutputDirectory>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>2.4.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-shade-plugin</artifactId>
          <version>2.4.3</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>templating-maven-plugin</artifactId>
          <version>1.0.0</version>
        </plugin>
        <plugin>
          <groupId>pl.project13.maven</groupId>
          <artifactId>git-commit-id-plugin</artifactId>
          <version>2.2.1</version>
          <configuration>
            <gitDescribe>
              <always>true</always>
            </gitDescribe>
          </configuration>
        </plugin>
        <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>3.5.1</version>
          <configuration>
            <source>${java.version}</source>
            <target>${java.version}</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>net.alchim31.maven</groupId>
          <artifactId>scala-maven-plugin</artifactId>
          <version>3.2.2</version>
        </plugin>
        <!-- disable surefire -->
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>2.7</version>
        </plugin>
        <!-- enable scalatest -->
        <plugin>
          <groupId>org.scalatest</groupId>
          <artifactId>scalatest-maven-plugin</artifactId>
          <version>1.0</version>
        </plugin>
        <plugin>
          <groupId>org.scalariform</groupId>
          <artifactId>scalariform-maven-plugin</artifactId>
          <version>0.1.4</version>
        </plugin>
        <plugin>
          <artifactId>exec-maven-plugin</artifactId>
          <groupId>org.codehaus.mojo</groupId>
          <version>1.3.2</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>build-helper-maven-plugin</artifactId>
          <version>1.10</version>
        </plugin>
      </plugins>
    </pluginManagement>
    <plugins>
      <plugin>
        <groupId>org.codehaus.mojo</groupId>
        <artifactId>build-helper-maven-plugin</artifactId>
        <executions>
          <execution>
            <id>add-source</id>
            <phase>generate-sources</phase>
            <goals>
              <goal>add-source</goal>
            </goals>
            <configuration>
              <sources>
                <source>src/main/scala</source>
              </sources>
            </configuration>
          </execution>
          <execution>
            <id>add-test-source</id>
            <phase>generate-test-sources</phase>
            <goals>
              <goal>add-test-source</goal>
            </goals>
            <configuration>
              <sources>
                <source>src/test/scala</source>
              </sources>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
        <executions>
          <execution>
            <id>scala-compile-first</id>
            <phase>process-resources</phase>
            <goals>
              <goal>compile</goal>
            </goals>
            <configuration>
              <args>
                <arg>-g:vars</arg>
              </args>
            </configuration>
          </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>${scala.version}</scalaVersion>
          <useZincServer>true</useZincServer>
          <args>
            <arg>-unchecked</arg>
            <arg>-optimise</arg>
            <arg>-deprecation</arg>
          </args>
          <jvmArgs>
            <jvmArg>-Xms64m</jvmArg>
            <jvmArg>-Xms1024m</jvmArg>
            <jvmArg>-Xmx1024m</jvmArg>
          </jvmArgs>
          <javacArgs>
            <javacArg>-source</javacArg>
            <javacArg>${java.version}</javacArg>
            <javacArg>-target</javacArg>
            <javacArg>${java.version}</javacArg>
          </javacArgs>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.scalariform</groupId>
        <artifactId>scalariform-maven-plugin</artifactId>
        <version>0.1.4</version>
        <executions>
          <execution>
            <id>default-cli</id>
            <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.bdgenomics.utils</groupId>
        <artifactId>utils-cli-spark2_2.11</artifactId>
        <version>${utils.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.deca</groupId>
        <artifactId>deca-core_2.11</artifactId>
        <version>${project.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.deca</groupId>
        <artifactId>deca-core_2.11</artifactId>
        <version>${project.version}</version>
        <type>test-jar</type>
        <scope>test</scope>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.utils</groupId>
        <artifactId>utils-misc-spark2_2.11</artifactId>
        <version>${utils.version}</version>
        <type>test-jar</type>
        <scope>test</scope>        
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.utils</groupId>
        <artifactId>utils-serialization-spark2_2.11</artifactId>
        <version>${utils.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.utils</groupId>
        <artifactId>utils-metrics-spark2_2.11</artifactId>
        <version>${utils.version}</version>
      </dependency>
      <dependency>
        <groupId>net.fnothaft</groupId>
        <artifactId>jsr203-s3a</artifactId>
        <version>0.0.1</version>
      </dependency>
      <dependency>
        <groupId>org.apache.hadoop</groupId>
        <artifactId>hadoop-client</artifactId>
        <version>${hadoop.version}</version>
        <scope>provided</scope>
        <exclusions>
          <exclusion>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
          </exclusion>
          <exclusion>
            <groupId>asm</groupId>
            <artifactId>asm</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.jboss.netty</groupId>
            <artifactId>netty</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.sonatype.sisu.inject</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>javax.servlet</groupId>
            <artifactId>*</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-core-spark2_2.11</artifactId>
        <version>${adam.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-cli-spark2_2.11</artifactId>
        <version>${adam.version}</version>
      </dependency>
      <dependency>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest_${scala.version.prefix}</artifactId>
        <version>2.2.6</version>
        <scope>test</scope>
      </dependency>
      <dependency>
        <groupId>commons-configuration</groupId>
        <artifactId>commons-configuration</artifactId>
        <version>1.10</version>
      </dependency>
      <dependency>
        <groupId>commons-io</groupId>
        <artifactId>commons-io</artifactId>
        <version>2.4</version>
      </dependency>
      <dependency>
        <groupId>args4j</groupId>
        <artifactId>args4j</artifactId>
        <version>2.0.31</version> <!-- note: version 2.32 is not binary compatible -->
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-core_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
        <scope>provided</scope>
      </dependency>
      <dependency>
        <groupId>org.apache.avro</groupId>
        <artifactId>avro</artifactId>
        <version>${avro.version}</version>
      </dependency>
      <dependency>
        <groupId>org.scalanlp</groupId>
        <artifactId>breeze_${scala.version.prefix}</artifactId>
        <version>${breeze.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-mllib_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
        <scope>provided</scope>
      </dependency>
    </dependencies>
  </dependencyManagement>

  <profiles>
    <profile>
      <id>distribution</id>
      <modules>
        <module>deca-core</module>
        <module>deca-cli</module>
        <!-- distribution should be last -->
        <module>deca-distribution</module>
      </modules>
      <build>
        <plugins>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <version>3.0.1</version>
            <executions>
              <execution>
                <id>attach-sources</id>
                <phase>package</phase>
                <goals>
                  <goal>jar-no-fork</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-javadoc-plugin</artifactId>
            <version>2.10.4</version>
            <executions>
              <execution>
                <id>attach-javadocs</id>
                <phase>package</phase>
                <goals>
                  <goal>jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
          <plugin>
            <groupId>net.alchim31.maven</groupId>
            <artifactId>scala-maven-plugin</artifactId>
            <executions>
              <execution>
                <id>scala-compile-first</id>
                <phase>process-resources</phase>
                <goals>
                  <goal>compile</goal>
                </goals>
                <configuration>
                  <args>
                    <arg>-g:vars</arg>
                  </args>
                </configuration>
              </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>package</phase>
                <goals>
                  <goal>doc-jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
    <profile>
      <id>coverage</id>
      <build>
        <plugins>
          <plugin>
            <groupId>org.scoverage</groupId>
            <artifactId>scoverage-maven-plugin</artifactId>
            <version>${scoverage.plugin.version}</version>
            <configuration>
              <scalaVersion>2.11.4</scalaVersion>
              <excludedPackages>org.bdgenomics.deca.Timers</excludedPackages>
              <aggregate>true</aggregate>
              <minimumCoverage>90</minimumCoverage>
              <failOnMinimumCoverage>false</failOnMinimumCoverage>
            </configuration>
          </plugin>
        </plugins>
      </build>
    </profile>
    <profile>
      <id>sonatype-oss-release</id>
      <build>
        <plugins>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-gpg-plugin</artifactId>
            <version>1.6</version>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
    <profile>
      <id>native-lgpl</id>
      <dependencyManagement>
	<dependencies>
	  <dependency>
            <groupId>org.scalanlp</groupId>
            <artifactId>breeze-natives_${scala.version.prefix}</artifactId>
            <version>${breeze.version}</version>
	  </dependency>
	</dependencies>
      </dependencyManagement>
    </profile>
  </profiles>
</project>