Description

<dependency>
    <groupId>de.charite.compbio</groupId>
    <artifactId>jannovar-vardbs</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-vardbs</artifactId>
    <packaging>jar</packaging>

    <name>${project.groupId}:${project.artifactId}</name>
    <description>jannovar-vardbs helps with using variant annotation databases, e.g. dbSNP</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>
        <!-- Simple logging for console -->
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>${htsjdk.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.tukaani</groupId>
                    <artifactId>xz</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <version>${guava.version}</version>
        </dependency>
        <dependency>
            <groupId>org.ini4j</groupId>
            <artifactId>ini4j</artifactId>
            <version>0.5.1</version>
        </dependency>
        <dependency>
            <groupId>de.charite.compbio</groupId>
            <artifactId>jannovar-core</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>de.charite.compbio</groupId>
            <artifactId>jannovar-htsjdk</artifactId>
            <version>${project.version}</version>
        </dependency>
        <dependency>
            <groupId>com.h2database</groupId>
            <artifactId>h2</artifactId>
            <version>${h2.version}</version>
        </dependency>
        <!-- Logging -->
        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-api</artifactId>
            <version>${log4j.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-core</artifactId>
            <version>${log4j.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. ${project.version} -->
                <filtering>true</filtering>
            </resource>
        </resources>
        <plugins>
            <!-- Make an executable jar and specify the main class and classpath -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.5</version>
                <configuration>
                    <archive>
                        <manifest>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib/</classpathPrefix>
                            <!-- set useUniqueVersions=false in order that the classpath has the
                                SNAPSHOT instead of the build number prefixed to the dependency -->
                            <useUniqueVersions>false</useUniqueVersions>
                            <mainClass>de.charite.compbio.jannovar.Jannovar</mainClass>
                        </manifest>
                    </archive>
                    <compilerArgument>-Xlint:all</compilerArgument>
                    <showWarnings>true</showWarnings>
                    <showDeprecation>true</showDeprecation>
                </configuration>
            </plugin>
            <!-- Specify the resources which need to be made accessible to the user -->
            <plugin>
                <artifactId>maven-resources-plugin</artifactId>
                <version>2.6</version>
                <executions>
                    <execution>
                        <id>copy-resources</id>
                        <phase>validate</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${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>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>