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/maven-v4_0_0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<parent>
		<artifactId>owlsim</artifactId>
		<groupId>org.monarchinitiative.owlsim</groupId>
		<version>3.0-SNAPSHOT</version>
	</parent>
	<artifactId>owlsim-core</artifactId>
	<packaging>jar</packaging>
	<name>owlsim-core</name>

	<properties>
		<jena.version>2.11.2</jena.version>
	</properties>

        <build>
          <plugins>
            <!-- Build a bin/owlsim.jar file with all dependencies -->
            <plugin>
              <groupId>org.apache.maven.plugins</groupId>
              <artifactId>maven-assembly-plugin</artifactId>
              <configuration>
                <finalName>owlsim</finalName>
                <appendAssemblyId>false</appendAssemblyId>
                <attach>false</attach>
                <outputDirectory>${project.parent.basedir}/bin</outputDirectory>
                <descriptorRefs>
                  <descriptorRef>jar-with-dependencies</descriptorRef>
                </descriptorRefs>
                <archive>
                  <manifest>
                    <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                    <mainClass>org.monarchinitiative.owlsim.compute.runner.RunEngine</mainClass>
                  </manifest>
                </archive>
              </configuration>
              <executions>
                <execution>
                  <id>make-assembly</id>
                  <phase>package</phase>
                  <goals>
                    <goal>single</goal>
                  </goals>
                </execution>
              </executions>
            </plugin>
            <plugin>
              <groupId>org.apache.maven.plugins</groupId>
              <artifactId>maven-failsafe-plugin</artifactId>
              <version>2.18.1</version>
              <executions>
                <execution>
                  <goals>
                    <goal>integration-test</goal>
                    <goal>verify</goal>
                  </goals>
                </execution>
              </executions>
            </plugin>
          </plugins>
        </build>

	<dependencies>
		<dependency>
			<groupId>org.apache.jena</groupId>
			<artifactId>jena-core</artifactId>
			<version>${jena.version}</version>
		</dependency>
		<dependency>
			<groupId>org.apache.jena</groupId>
			<artifactId>jena-arq</artifactId>
			<version>${jena.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-apibinding</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-api</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-contract</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-distribution</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-impl</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-parsers</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-tools</artifactId>
			<version>${owlapi.version}</version>
		</dependency>
		<dependency>
			<groupId>log4j</groupId>
			<artifactId>log4j</artifactId>
			<version>1.2.17</version>
			<exclusions>
				<exclusion>
					<artifactId>mail</artifactId>
					<groupId>javax.mail</groupId>
				</exclusion>
				<exclusion>
					<artifactId>jms</artifactId>
					<groupId>javax.jms</groupId>
				</exclusion>
				<exclusion>
					<artifactId>jmxtools</artifactId>
					<groupId>com.sun.jdmk</groupId>
				</exclusion>
				<exclusion>
					<artifactId>jmxri</artifactId>
					<groupId>com.sun.jmx</groupId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
			<groupId>org.apache.ant</groupId>
			<artifactId>ant</artifactId>
			<version>1.8.2</version>
		</dependency>
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.2</version>
		</dependency>
		<dependency>
			<groupId>org.semanticweb.elk</groupId>
			<artifactId>elk-owlapi</artifactId>
			<version>0.4.1</version>
		</dependency>
		<dependency>
			<groupId>com.google.code.gson</groupId>
			<artifactId>gson</artifactId>
			<version>2.2.4</version>
		</dependency>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>jfact</artifactId>
			<version>1.0.0</version>
		</dependency>
		<dependency>
			<groupId>jline</groupId>
			<artifactId>jline</artifactId>
			<version>0.9.93</version>
			<exclusions>
				<exclusion>
					<groupId>junit</groupId>
					<artifactId>junit</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
			<groupId>org.apache.geronimo.specs</groupId>
			<artifactId>geronimo-javamail_1.4_spec</artifactId>
			<version>1.6</version>
		</dependency>
		<dependency>
			<groupId>com.googlecode.javaewah</groupId>
			<artifactId>JavaEWAH</artifactId>
			<version>0.7.7</version>
		</dependency>
		<dependency>
		  <groupId>commons-validator</groupId>
		  <artifactId>commons-validator</artifactId>
		  <version>1.4.0</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.6.1</version>
		</dependency>
		<dependency>
		    <groupId>org.prefixcommons</groupId>
		    <artifactId>curie-util</artifactId>
		    <version>0.0.1</version>
		</dependency>
	</dependencies>


</project>