<?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/maven-v4_0_0.xsd">
  <parent>
    <artifactId>Jannovar</artifactId>
    <groupId>de.charite.compbio</groupId>
    <version>0.14</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>jannovar-cli</artifactId>
  <name>${project.groupId}:${project.artifactId}</name>
  <description>jannovar-cli is the command line interface for Jannovar</description>
  <url>http://charite.github.io/jannovar/</url>
  <build>
    <resources>
      <resource>
        <filtering>true</filtering>
        <directory>src/main/resources</directory>
      </resource>
    </resources>
    <plugins>
      <plugin>
        <artifactId>maven-jar-plugin</artifactId>
        <version>2.5</version>
        <configuration>
          <archive>
            <manifest>
              <addClasspath>true</addClasspath>
              <classpathPrefix>lib/</classpathPrefix>
              <useUniqueVersions>false</useUniqueVersions>
              <mainClass>de.charite.compbio.jannovar.Jannovar</mainClass>
            </manifest>
          </archive>
          <compilerArgument>-Xlint:all</compilerArgument>
          <showWarnings>true</showWarnings>
          <showDeprecation>true</showDeprecation>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-shade-plugin</artifactId>
        <version>2.2</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <transformers>
                <transformer>
                  <mainClass>de.charite.compbio.jannovar.Jannovar</mainClass>
                </transformer>
              </transformers>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-resources-plugin</artifactId>
        <version>2.6</version>
        <executions>
          <execution>
            <id>copy-resources</id>
            <phase>validate</phase>
            <goals>
              <goal>copy-resources</goal>
            </goals>
            <configuration>
              <outputDirectory>${project.build.directory}/resources</outputDirectory>
              <resources>
                <resource>
                  <directory>src/resources</directory>
                  <filtering>true</filtering>
                  <includes>
                    <include>application.properties</include>
                    <include>example.settings</include>
                    <include>test.settings</include>
                    <include>log4j2.xml</include>
                  </includes>
                </resource>
              </resources>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <version>2.4</version>
        <executions>
          <execution>
            <id>make-assembly</id>
            <phase>package</phase>
            <goals>
              <goal>single</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <descriptors>
            <descriptor>src/assembly/dep.xml</descriptor>
          </descriptors>
        </configuration>
      </plugin>
    </plugins>
  </build>
  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.11</version>
      <scope>test</scope>
      <exclusions>
        <exclusion>
          <artifactId>hamcrest-core</artifactId>
          <groupId>org.hamcrest</groupId>
        </exclusion>
      </exclusions>
    </dependency>
  </dependencies>
  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  </properties>
</project>

