pom.xml

<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>au.edu.wehi</groupId>
	<artifactId>gridss</artifactId>
	<packaging>jar</packaging>
	<version>${revision}-gridss</version>
	<name>gridss</name>
	<url>https://github.com/PapenfussLab/gridss</url>
	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<revision>0.0.1-SNAPSHOT</revision>
	</properties>
	<licenses>
		<license>
			<name>GNU General Public License (GPL)</name>
			<url>http://www.gnu.org/licenses/gpl.txt</url>
		</license>
	</licenses>
	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>
				<version>3.2.0</version>
				<configuration>
					<archive>
						<manifest>
							<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
							<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
						</manifest>
						<manifestEntries>
							<Multi-Release>true</Multi-Release>
						</manifestEntries>
					</archive>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.9.0</version>
				<configuration>
					<source>1.8</source>
					<target>1.8</target>
					<release>8</release>
					<!-- don't have multi-release output in the java8 configuration because we want it to be in the default location at the jar root -->
					<!--<multiReleaseOutput>true</multiReleaseOutput>-->
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-shade-plugin</artifactId>
				<version>3.2.4</version>
				<executions>
					<execution>
						<phase>package</phase>
						<goals>
							<goal>shade</goal>
						</goals>
						<configuration>
							<finalName>${project.artifactId}-${project.version}-jar-with-dependencies</finalName>
							<transformers>
								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
									<mainClass>>gridss.CallVariants</mainClass>
								</transformer>
							</transformers>
							<artifactSet>
								<excludes>
								</excludes>
							</artifactSet>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.19.1</version>
				<configuration>
					<excludedGroups>au.edu.wehi.idsv.Hg19Tests,au.edu.wehi.idsv.Hg38Tests,au.edu.wehi.idsv.EColiTests,au.edu.wehi.idsv.alignment.ExternalAlignerTests,au.edu.wehi.idsv.alignment.JniAlignerTests</excludedGroups>
					<argLine>-Xmx4g</argLine>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>0.7.7.201606060606</version>
				<executions>
					<execution>
						<id>default-prepare-agent</id>
						<goals>
							<goal>prepare-agent</goal>
						</goals>
					</execution>
					<execution>
						<id>default-report</id>
						<phase>prepare-package</phase>
						<goals>
							<goal>report</goal>
						</goals>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.eluder.coveralls</groupId>
				<artifactId>coveralls-maven-plugin</artifactId>
				<version>4.2.0</version>
			</plugin>
		</plugins>
	</build>
	<repositories>
		<repository>
			<id>project.local</id>
			<name>project</name>
			<url>file:${project.basedir}/repo</url>
		</repository>
	</repositories>
	<dependencies>
		<dependency>
			<groupId>jaligner</groupId>
			<artifactId>jaligner</artifactId>
			<version>1.0</version>
		</dependency>
		<dependency>
			<groupId>ssw</groupId>
			<artifactId>ssw</artifactId>
			<version>1.0</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.13.1</version>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<version>30.0-jre</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-lang3</artifactId>
			<version>3.10</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.6.1</version>
		</dependency>
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.7</version>
		</dependency>
		<dependency>
			<groupId>commons-configuration</groupId>
			<artifactId>commons-configuration</artifactId>
			<version>1.10</version>
		</dependency>
		<dependency>
			<groupId>it.uniroma1.dis.wsngroup.gexf4j</groupId>
			<artifactId>gexf4j</artifactId>
			<version>1.0.0</version>
		</dependency>
		<dependency>
			<groupId>it.unimi.dsi</groupId>
			<artifactId>fastutil</artifactId>
			<version>8.3.1</version>
		</dependency>
		<dependency>
			<groupId>net.sf.trove4j</groupId>
			<artifactId>trove4j</artifactId>
			<version>3.0.3</version>
		</dependency>
		<dependency>
			<groupId>com.github.samtools</groupId>
			<artifactId>htsjdk</artifactId>
			<version>2.23.0</version>
		</dependency>
		<dependency>
			<groupId>com.github.broadinstitute</groupId>
			<artifactId>picard</artifactId>
			<version>2.23.2</version>
		</dependency>
		<dependency>
			<groupId>org.broadinstitute</groupId>
			<artifactId>barclay</artifactId>
			<version>3.0.0</version>
		</dependency>
		<dependency>
			<groupId>org.broadinstitute</groupId>
			<artifactId>gatk-bwamem-jni</artifactId>
			<version>1.0.5</version>
		</dependency>
		<dependency>
			<groupId>org.broadinstitute</groupId>
			<artifactId>gatk-minimap2-jni</artifactId>
			<version>1.0.2</version>
		</dependency>
		<dependency>
			<groupId>com.intel.gkl</groupId>
			<artifactId>gkl</artifactId>
			<version>0.8.6</version>
		</dependency>
	</dependencies>
	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-bom</artifactId>
				<version>2.17.1</version>
				<scope>import</scope>
				<type>pom</type>
			</dependency>
		</dependencies>
	</dependencyManagement>
	<scm>
		<developerConnection>Daniel Cameron</developerConnection>
		<url>https://github.com/PapenfussLab/gridss</url>
	</scm>
</project>