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>
	
	<properties>
		<bundle.symbolicName>eXamine</bundle.symbolicName>
		<bundle.namespace>org.cytoscape.examine.internal</bundle.namespace>
		<cytoscape.api.version>3.0.0</cytoscape.api.version>
		<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
		<osgi.api.version>4.2.0</osgi.api.version>
	</properties>
	
	<groupId>org.cytoscape.examine</groupId>
	<artifactId>examine</artifactId>
	<packaging>bundle</packaging>
	<name>eXamine</name>

	<version>1.0</version>
  
  	<repositories>
  		<repository>
			<id>custom_rep</id>
			<name>Custom Repository</name>
			<url>file://${project.basedir}/lib</url>
		</repository>
		<repository>
			<id>cytoscape_snapshots</id>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>false</enabled>
			</releases>
			<name>Cytoscape Snapshots</name>
			<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
		</repository>
		<repository>
			<id>cytoscape_releases</id>
			<snapshots>
				<enabled>false</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
			<name>Cytoscape Releases</name>
			<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
		</repository>
	</repositories>

	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.felix</groupId>
				<artifactId>maven-bundle-plugin</artifactId>
				<version>${maven-bundle-plugin.version}</version>
				<extensions>true</extensions>
				<configuration>
					<instructions>
						<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
						<Bundle-Version>${project.version}</Bundle-Version>
						<Export-Package>!${bundle.namespace}.*</Export-Package>
						<Private-Package>${bundle.namespace}.*</Private-Package>
						<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
                                                
                                                <!-- embed all compile and runtime scope dependencies -->
                                                <Embed-Dependency>
                                                    jgrapht-jdk1.5;groupId=org.jgrapht;inline=true,
                                                    opencsv;groupId=net.sf.opencsv;inline=true,
                                                    Aether2D;groupId=org.cytoscape.examine;inline=true,
                                                    processing;groupId=org.cytoscape.examine;inline=true,
                                                    jts;groupId=com.vividsolutions;inline=true
                                                </Embed-Dependency>                                               
                                                <Import-Package>*;resolution:=optional</Import-Package>
					</instructions>
				</configuration>
			</plugin>
		</plugins>
	</build>
    
  	<dependencies>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>swing-application-api</artifactId>
			<version>${cytoscape.api.version}</version>
		</dependency>
  	   <dependency>
  	      <groupId>org.cytoscape</groupId>
  	      <artifactId>group-api</artifactId>
  	      <version>${cytoscape.api.version}</version>
  	   </dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>work-api</artifactId>
			<version>${cytoscape.api.version}</version>
		</dependency>
			<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>service-api</artifactId>
			<version>${cytoscape.api.version}</version>
		</dependency>
		
		<dependency>
			<groupId>org.osgi</groupId>
			<artifactId>org.osgi.core</artifactId>
			<version>${osgi.api.version}</version>
		</dependency>
  	   <dependency>
  	      <groupId>org.jgrapht</groupId>
  	      <artifactId>jgrapht-jdk1.5</artifactId>
  	      <version>0.7.3</version>
  	   </dependency>
  	   <dependency>
  	      <groupId>net.sf.opencsv</groupId>
  	      <artifactId>opencsv</artifactId>
  	      <version>2.3</version>
  	   </dependency>
  	   <dependency>
  	      <groupId>com.vividsolutions</groupId>
  	      <artifactId>jts</artifactId>
  	      <version>1.13</version>
  	   </dependency>
  	</dependencies>
  
  	<description>eXamine is a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. eXamine extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours.</description>
</project>