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pom.xml
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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.hammerlab.guacamole</groupId>
<artifactId>guacamole</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>guacamole: variant caller</name>
<properties>
<adam.version>0.19.0</adam.version>
<bdg-formats.version>0.7.0</bdg-formats.version>
<java.version>1.8</java.version>
<scala.version>2.10.5</scala.version>
<scala.version.prefix>2.10</scala.version.prefix>
<hadoop.version>2.7.0</hadoop.version>
<spark.version>1.6.1</spark.version>
<maven.release.plugin.version>2.4.1</maven.release.plugin.version>
<shade.plugin.version>2.1</shade.plugin.version>
<scoverage.plugin.version>1.1.1</scoverage.plugin.version>
</properties>
<licenses>
<license>
<name>Apache License</name>
<url>https://raw.github.com/hammerlab/guacamole/master/LICENSE</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<connection>scm:git:git@github.com:hammerlab/guacamole.git</connection>
<developerConnection>scm:git:git@github.com:hammerlab/guacamole.git</developerConnection>
<url>scm:git:git@github.com:hammerlab/guacamole.git</url>
<tag>HEAD</tag>
</scm>
<build>
<outputDirectory>target/scala-${scala.version}/classes</outputDirectory>
<testOutputDirectory>target/scala-${scala.version}/test-classes</testOutputDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${shade.plugin.version}</version>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>org.hammerlab.guacamole.Main</mainClass>
</transformer>
<!-- Akka (which Spark depends on) needs this reference.conf munging in order to work correctly in -->
<!-- shaded JARs, cf. http://stackoverflow.com/questions/31011243/#31011315 -->
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>reference.conf</resource>
</transformer>
<!-- Necessary for Hadoop to load local files correctly, cf. http://stackoverflow.com/a/27532248/544236 -->
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/LICENSE</exclude>
<exclude>META-INF/license</exclude>
</excludes>
</filter>
</filters>
<artifactSet>
<excludes>
<exclude>org.eclipse.jdt:*</exclude>
<exclude>org.scalatest:*</exclude>
<exclude>org.apache.maven:lib:tests</exclude>
</excludes>
</artifactSet>
</configuration>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.1.5</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
<configuration>
<args>
<arg>-g:vars</arg>
</args>
</configuration>
</execution>
<execution>
<id>scala-test-compile-first</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>attach-scaladocs</id>
<phase>verify</phase>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<recompileMode>incremental</recompileMode>
<useZincServer>false</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>
<!-- 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</version>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>GuacamoleTestSuite.txt</filereports>
<argLine>-Xmx4g -XX:MaxPermSize=256m</argLine>
<stdout>F</stdout>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>${maven.release.plugin.version}</version>
<configuration>
<branchName>branch-@{project.version}</branchName>
<goals>deploy</goals>
<tagNameFormat>guacamole-@{project.version}</tagNameFormat>
</configuration>
<dependencies>
<dependency>
<groupId>org.apache.maven.scm</groupId>
<artifactId>maven-scm-provider-gitexe</artifactId>
<version>1.8.1</version>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
<distributionManagement>
<snapshotRepository>
<id>sonatype-nexus-snapshots</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</snapshotRepository>
<repository>
<id>sonatype-nexus-staging</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<repositories>
<repository>
<id>sonatype-nexus-snapshots</id>
<name>Sonatype Nexus Snapshots</name>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central</id>
<url>http://repo1.maven.org/maven2</url>
</repository>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>spire</id>
<url>http://dl.bintray.com/non/maven</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
<version>2.21</version>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>[2.0.29,)</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core_${scala.version.prefix}</artifactId>
<version>${adam.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-formats</groupId>
<artifactId>bdg-formats</artifactId>
<version>${bdg-formats.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.qc-metrics</groupId>
<artifactId>qc-metrics-core_${scala.version.prefix}</artifactId>
<version>0.0.1</version>
</dependency>
<dependency>
<groupId>colt</groupId>
<artifactId>colt</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>org.spire-math</groupId>
<artifactId>spire_${scala.version.prefix}</artifactId>
<version>0.11.0</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-mllib_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.scalanlp</groupId>
<artifactId>breeze_${scala.version.prefix}</artifactId>
<version>0.11.2</version>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>htsjdk</artifactId>
<version>1.118</version>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>hadoop-bam</artifactId>
<version>7.0.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>${hadoop.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
</dependency>
<dependency>
<groupId>org.spire-math</groupId>
<artifactId>debox_${scala.version.prefix}</artifactId>
<version>0.6.0</version>
</dependency>
<dependency>
<groupId>com.assembla.scala-incubator</groupId>
<artifactId>graph-core_${scala.version.prefix}</artifactId>
<version>1.9.1</version>
</dependency>
<dependency>
<groupId>org.hammerlab</groupId>
<artifactId>magic-rdds</artifactId>
<version>1.0.0-20160819.031655-6</version>
</dependency>
<!-- Test deps -->
<dependency>
<groupId>com.holdenkarau</groupId>
<artifactId>spark-testing-base_${scala.version.prefix}</artifactId>
<version>${spark.version}_0.3.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-misc</artifactId>
<version>0.1.1</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.5</version>
<scope>test</scope>
</dependency>
</dependencies>
<profiles>
<profile>
<!-- Default profile: build Guacamole jar with shaded Guava. -->
<id>guac</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>default</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>guacamole-${project.version}</finalName>
<relocations>
<relocation>
<pattern>com.google.common</pattern>
<shadedPattern>org.hammerlab.guavarelocated</shadedPattern>
<includes>
<include>com.google.common.**</include>
</includes>
</relocation>
</relocations>
<artifactSet>
<includes>
<include>org.hammerlab.guacamole:*</include>
<include>com.google.guava:*</include>
</includes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- Only build coverage in when we want to run coverage -->
<profile>
<id>coverage</id>
<!-- Activate when being built by travis CI. -->
<activation>
<property>
<name>env.TRAVIS</name>
<value>true</value>
</property>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<version>4.2.0</version>
<configuration>
<sourceDirectories>
<sourceDirectory>src/main/scala</sourceDirectory>
</sourceDirectories>
<coberturaReports>
<coberturaReport>${basedir}/target/cobertura.xml</coberturaReport>
</coberturaReports>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>cluster</id>
<dependencies>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>${hadoop.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>
</profile>
<profile>
<id>release</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.1.2</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<!-- "uber" profile: build a JAR with Guacamole and all transitive dependencies shaded, and Guava relocated. -->
<id>uber</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>deps</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>guacamole-with-deps-${project.version}</finalName>
<relocations>
<relocation>
<pattern>com.google.common</pattern>
<shadedPattern>org.hammerlab.guavarelocated</shadedPattern>
<includes>
<include>com.google.common.**</include>
</includes>
</relocation>
</relocations>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<!-- "deps" profile: build a JAR with just Guacamole's transitive dependencies. -->
<id>deps</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>deps</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>guacamole-deps-only-${project.version}</finalName>
<artifactSet>
<excludes>
<exclude>org.hammerlab.guacamole:*</exclude>
</excludes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>