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pom.xml
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<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">
<modelVersion>4.0.0</modelVersion>
<groupId>ch.ethz.bsse</groupId>
<artifactId>consensusfixer</artifactId>
<version>0.4</version>
<packaging>jar</packaging>
<name>ConsensusFixer</name>
<developers>
<developer>
<id>toepfera</id>
<name>Armin Töpfer</name>
<email>[email protected]</email>
</developer>
</developers>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<excludes>
<exclude>**/haplotypes/*</exclude>
</excludes>
<archive>
<manifest>
<mainClass>ch.ethz.bsse.cf.Startup</mainClass>
<addDefaultImplementationEntries>
true
</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<mode>development</mode>
<url>${project.url}</url>
<author>value</author>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>com.jolira</groupId>
<artifactId>onejar-maven-plugin</artifactId>
<version>1.4.4</version>
<executions>
<execution>
<configuration>
<!-- Optional -->
<onejarVersion>0.97</onejarVersion>
<!-- Optional, default is false -->
<attachToBuild>true</attachToBuild>
<!-- Optional, default is "onejar" -->
<classifier>full</classifier>
<filename>ConsensusFixer.jar</filename>
</configuration>
<goals>
<goal>one-jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
<dependency>
<scope>compile</scope>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>2.0.16</version>
</dependency>
<!-- <dependency>
<groupId>org.javatuples</groupId>
<artifactId>javatuples</artifactId>
<version>1.2</version>
</dependency>-->
<dependency>
<groupId>net.sf</groupId>
<artifactId>samtools</artifactId>
<version>1.9.6</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>14.0.1</version>
</dependency>
</dependencies>
<pluginRepositories>
<pluginRepository>
<id>onejar-maven-plugin.googlecode.com</id>
<url>http://onejar-maven-plugin.googlecode.com/svn/mavenrepo</url>
</pluginRepository>
</pluginRepositories>
<repositories>
<repository>
<id>ibiblio</id>
<url>http://www.ibiblio.org/maven/</url>
</repository>
<repository>
<id>snapshots</id>
<url>https://repository.apache.org/content/repositories/snapshots</url>
</repository>
<repository>
<id>boundary-site</id>
<url>http://maven.boundary.com/artifactory/repo</url>
</repository>
<!-- <repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>-->
</repositories>
</project>