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>com.thaze</groupId>
	<artifactId>peakmatch</artifactId>
	<version>0.0.1-SNAPSHOT</version>
	<packaging>jar</packaging>
	<name>peakmatch</name>

	<url>https://github.com/simonrodgers/peakmatch-xcorr</url>

	<developers>
		<developer>
			<name>Simon Rodgers</name>
		</developer>
	</developers>

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

	<dependencies>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
            <version>2.2</version>
        </dependency>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.1</version>
        </dependency>
		<dependency>
			<groupId>commons-lang</groupId>
			<artifactId>commons-lang</artifactId>
			<version>2.3</version>
		</dependency>
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.7</version>
		</dependency>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<version>11.0.2</version>
		</dependency>
		<dependency>
			<groupId>joda-time</groupId>
			<artifactId>joda-time</artifactId>
			<version>1.6</version>
		</dependency>
		<dependency>
			<groupId>net.sf.json-lib</groupId>
			<artifactId>json-lib</artifactId>
			<version>2.4</version>
			<classifier>jdk15</classifier>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.13.1</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>vanilla.java</groupId>
			<artifactId>chronicle</artifactId>
			<version>1.2-SNAPSHOT</version>
			<!-- don't add system scope, it screws up assembly. just install on the remote system:
				mvn install:install-file -Dfile=lib/chronicle-1.2-SNAPSHOT.jar -DgroupId=vanilla.java -DartifactId=chronicle -Dversion=1.2-SNAPSHOT -Dpackaging=jar
			<scope>system</scope> 
			<systemPath>${basedir}/lib/chronicle-1.2-SNAPSHOT.jar</systemPath> 
			-->
		</dependency>
<!--
        <dependency>
            <groupId>edu.berkeley.compbio</groupId>
            <artifactId>ml</artifactId>
            <version>0.9</version>
        </dependency>-->
        <dependency>
            <groupId>org.functionaljava</groupId>
            <artifactId>functionaljava</artifactId>
            <version>3.0</version>
        </dependency>
        <dependency>
            <groupId>jgrapht</groupId>
            <artifactId>jgrapht</artifactId>
            <version>0.7.3</version>
        </dependency>



    </dependencies>

	<build>
		<plugins>
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<configuration>
					<archive>
						<manifest>
							<mainClass>com.thaze.peakmatch.XCorrProcessor</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
					<finalName>peakmatch</finalName>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>2.5.1</version>
				<configuration>
					<source>1.7</source>
					<target>1.7</target>
				</configuration>
			</plugin>
		</plugins>
	</build>

</project>