Description

<dependency>
    <groupId>de.charite.compbio</groupId>
    <artifactId>jannovar-htsjdk</artifactId>
    <version>0.41</version>
</dependency>

<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>

    <artifactId>jannovar-htsjdk</artifactId>
    <packaging>jar</packaging>

    <name>${project.groupId}:${project.artifactId}</name>
    <description>jannovar-htsjdk is the module for bridging between Jannovar and HTSJDK</description>
    <url>http://charite.github.io/jannovar/</url>

    <parent>
        <groupId>de.charite.compbio</groupId>
        <artifactId>Jannovar</artifactId>
        <version>0.41</version>
    </parent>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.7</version>
        </dependency>
        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
            <version>3.3</version>
        </dependency>
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <version>${guava.version}</version>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>${htsjdk.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.tukaani</groupId>
                    <artifactId>xz</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>de.charite.compbio</groupId>
            <artifactId>jannovar-core</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>de.charite.compbio</groupId>
            <artifactId>jannovar-hgvs</artifactId>
            <version>${project.version}</version>
        </dependency>
    </dependencies>

    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <!--Use filtering so that maven will replace placeholders 
                    with values from the pom e.g. ${project.version} -->
                <filtering>true</filtering>
            </resource>
        </resources>
        <plugins>
            <!-- Specify the dependencies to copy -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.8</version>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/lib</outputDirectory>
                            <overWriteReleases>false</overWriteReleases>
                            <overWriteSnapshots>false</overWriteSnapshots>
                            <overWriteIfNewer>true</overWriteIfNewer>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <!-- Specify the resources which need to be made accessible to 
                the user -->
            <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/main/resources</directory>
                                    <!--Use filtering so that maven will 
                                        replace placeholders with values from the pom e.g. ${project.version} -->
                                    <filtering>true</filtering>
                                    <includes>
                                        <include>project.properties</include>
                                        <include>application.properties</include>
                                        <include>example.settings</include>
                                        <include>test.settings</include>
                                        <include>log4j2.xml</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>