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pom.xml
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<?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.adam</groupId>
<artifactId>adam-parent_2.10</artifactId>
<version>0.20.1-SNAPSHOT</version>
<packaging>pom</packaging>
<name>ADAM_${scala.version.prefix}</name>
<description>A fast, scalable genome analysis system</description>
<url>http://bdgenomics.org/</url>
<properties>
<java.version>1.8</java.version>
<avro.version>1.8.0</avro.version>
<scala.version>2.10.6</scala.version>
<scala.version.prefix>2.10</scala.version.prefix>
<spark.version>1.6.3</spark.version>
<parquet.version>1.8.1</parquet.version>
<!-- Edit the following line to configure the Hadoop (HDFS) version. -->
<hadoop.version>2.7.3</hadoop.version>
<hadoop-bam.version>7.7.0</hadoop-bam.version>
<slf4j.version>1.7.21</slf4j.version>
<bdg-formats.version>0.10.1</bdg-formats.version>
<bdg-utils.version>0.2.10</bdg-utils.version>
<htsjdk.version>2.5.0</htsjdk.version>
<scoverage.plugin.version>1.1.1</scoverage.plugin.version>
</properties>
<modules>
<module>adam-core</module>
<module>adam-apis</module>
<module>adam-cli</module>
<module>adam-assembly</module>
</modules>
<licenses>
<license>
<name>Apache License</name>
<url>https://raw.github.com/bigdatagenomics/adam/master/LICENSE.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<connection>scm:git:[email protected]:bigdatagenomics/adam.git</connection>
<developerConnection>scm:git:[email protected]:bigdatagenomics/adam.git</developerConnection>
<url>scm:git:[email protected]:bigdatagenomics/adam.git</url>
<tag>master</tag>
</scm>
<developers>
<developer>
<id>massie</id>
<name>Matt Massie</name>
<email>[email protected]</email>
<url>http://www.cs.berkeley.edu/~massie</url>
<organization>U.C. Berkeley Computer Science</organization>
<organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
</developer>
</developers>
<issueManagement>
<system>github</system>
<url>https://github.com/bigdatagenomics/adam/issues</url>
</issueManagement>
<build>
<outputDirectory>target/${scala.version}/classes</outputDirectory>
<testOutputDirectory>target/${scala.version}/test-classes</testOutputDirectory>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5.5</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.2</version>
<configuration>
<mavenExecutorId>forked-path</mavenExecutorId>
<useReleaseProfile>false</useReleaseProfile>
<arguments>-Psonatype-oss-release</arguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.2</version>
</plugin>
<plugin>
<groupId>org.apache.avro</groupId>
<artifactId>avro-maven-plugin</artifactId>
<version>${avro.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>2.6.1</version>
</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>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.4.1</version>
<executions>
<execution>
<id>enforce-versions</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>[3.1.1,)</version>
<message>ADAM requires Maven 3.1.1 or greater</message>
</requireMavenVersion>
<requireJavaVersion>
<version>[1.8,)</version>
<message>ADAM requires Java 1.8 or greater</message>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>templating-maven-plugin</artifactId>
<version>1.0.0</version>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<version>1.0</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>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
</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>[email protected]</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.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.10</version>
</plugin>
<plugin>
<groupId>org.scalariform</groupId>
<artifactId>scalariform-maven-plugin</artifactId>
<version>0.1.4</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<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>${java.version}</javacArg>
</javacArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.scalariform</groupId>
<artifactId>scalariform-maven-plugin</artifactId>
<executions>
<execution>
<id>default-cli</id>
<goals>
<goal>format</goal>
</goals>
<configuration>
<alignParameters>true</alignParameters>
<alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
<doubleIndentClassDeclaration>true</doubleIndentClassDeclaration>
<preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
<version>2.24.0</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-formats</groupId>
<artifactId>bdg-formats</artifactId>
<version>${bdg-formats.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>it.unimi.dsi</groupId>
<artifactId>fastutil</artifactId>
<version>6.6.5</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core_${scala.version.prefix}</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core_${scala.version.prefix}</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-cli_${scala.version.prefix}</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-apis_${scala.version.prefix}</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-apis_${scala.version.prefix}</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
<type>test-jar</type>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.apache.spark</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.spark</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-cli_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-intervalrdd_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-io_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-metrics_${scala.version.prefix}</artifactId>
<version>${bdg-utils.version}</version>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>${hadoop.version}</version>
<scope>provided</scope>
<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>servlet-api</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-mapreduce</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
<version>${avro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<artifactId>parquet-avro</artifactId>
<version>${parquet.version}</version>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<!-- This library has no Scala 2.11 version, but using the 2.10 version seems to work. -->
<artifactId>parquet-scala_2.10</artifactId>
<version>${parquet.version}</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>hadoop-bam</artifactId>
<version>${hadoop-bam.version}</version>
<exclusions>
<exclusion>
<groupId>org.seqdoop</groupId>
<artifactId>htsjdk</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.version}</version>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>2.0.31</version> <!-- note: version 2.32 is not binary compatible -->
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<version>2.2.6</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.2</version>
</dependency>
<dependency>
<groupId>com.netflix.servo</groupId>
<artifactId>servo-core</artifactId>
<version>0.10.0</version> <!-- note: versions 0.11.0+ (currently 0.12.3) are jdk8-only -->
<exclusions>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>16.0.1</version> <!-- note: version 17.0 breaks hadoop 2.6+ at runtime -->
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.codingwell</groupId>
<artifactId>scala-guice_${scala.version.prefix}</artifactId>
<version>4.0.1</version>
</dependency>
</dependencies>
</dependencyManagement>
<profiles>
<profile>
<id>distribution</id>
<modules>
<module>adam-core</module>
<module>adam-apis</module>
<module>adam-cli</module>
<module>adam-assembly</module>
<!-- distribution should be last -->
<module>distribution</module>
</modules>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.4</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>package</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<executions>
<execution>
<id>attach-javadocs</id>
<phase>package</phase>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
<configuration>
<args>
<arg>-g:vars</arg>
</args>
</configuration>
</execution>
<execution>
<id>scala-test-compile-first</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>attach-scaladocs</id>
<phase>package</phase>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<aggregate>true</aggregate>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<!-- Only sign artifacts when we are performing a release, not snapshots -->
<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>
</profiles>
</project>