/
pom.xml
126 lines (120 loc) · 5.18 KB
/
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>
<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>0.42-SNAPSHOT</version>
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.16.1</version>
</dependency>
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.10.0</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. ${project.version} -->
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<!-- Specify the dependencies to copy -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.6.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${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>3.3.1</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>