pom-jalview-all.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>JalScape</bundle.symbolicName>
		<bundle.namespace>org.jalview.jalscape.internal</bundle.namespace>
		<cytoscape.api.version>3.1.0-SNAPSHOT</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.jalview</groupId>
	<artifactId>jalscape</artifactId>
	<packaging>bundle</packaging>
	<name>${bundle.symbolicName}</name>

	<version>0.9.0</version>

	<build>

	<plugins>
		<plugin>
			<artifactId>maven-antrun-plugin</artifactId>
			<executions>
				<execution>
					<id>validate</id>
					<phase>validate</phase>
					<configuration>
						<tasks>
							<ant dir="jalview" antfile="build.xml" target="makedist" />
							<unzip dest="${project.build.outputDirectory}/jalview_classes">
								<patternset>
									<include name="**/*.*" />
                <exclude name="META-INF/*.MF"/>
                <exclude name="META-INF/*.SF"/>
                <exclude name="META-INF/*.DSA"/>
                <exclude name="META-INF/*.RSA"/>
								</patternset>
								<fileset dir="${basedir}/jalview/dist">
									<include name="**/*.jar" />
								</fileset>
							</unzip>
<!-- 							<delete>
							<fileset dir="${project.build.outputDirectory}/jalview_classes/META-INF/">
							 <include name="**.SF"/>
							 <include name="**.DSA"/>
               <include name="**.RSA"/>
               
							</fileset>
							<includes
							</delete> -->
							<jar basedir="${project.build.outputDirectory}/jalview_classes"
	destfile="${project.build.outputDirectory}/jalview-all.jar" excludes="META-INF/*.SF">
	<manifest>
		<attribute name="Main-Class" value="jalview.bin.Jalview" />
	</manifest>
</jar>
								<exec>
								mvn deploy:deploy-file -Durl=file:///Users/jimp/git/JalScape/repo/ -Dfile=${project.build.outputDirectory}/jalview-all.jar -DgroupId=org.jalview -DartifactId=jalview-all -Dpackaging=jar  -Dversion=2.8   
								</exec>
			 <!-- 			<mvn> 
								<arg value="deploy:deploy-file" />
								<arg value="-Durl=file:///Users/jimp/git/JalScape/repo/" />
								<arg value="-Dfile=${project.build.outputDirectory}/jalview-all.jar" />
								<arg value="-DgroupId=org.jalview" />
								<arg value="-DartifactId=jalview-all" />
								<arg value="-Dpackaging=jar" />
								<arg value="-Dversion=2.8" />
							</mvn> --> 
						</tasks>
					</configuration>
					<goals>
						<goal>run</goal>
					</goals>
				</execution>
			</executions>
		</plugin>
		<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>
				</instructions>
			</configuration>
		</plugin>
  <!-- <plugin>
	<groupId>org.apache.maven.plugins</groupId>
	<artifactId>maven-shade-plugin</artifactId>
	<version>1.4</version>
	<executions>
		<execution>
			<phase>package</phase>
			<goals>
				<goal>shade</goal>
			</goals>
			<configuration>
				<artifactSet>
					<includes>
						<include>jalview:jalview</include>
					</includes>
				</artifactSet>
				<minimizeJar>true</minimizeJar>
			</configuration>
		</execution>
	</executions>
</plugin> -->
      <!-- plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-shade-plugin</artifactId>
        <version>1.4</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <artifactSet>
                <includes>
                  <include>org.openscience.cdk:*</include>
                </includes>
              </artifactSet>
              <minimizeJar>true</minimizeJar>
            </configuration>
          </execution>
        </executions>
      </plugin -->
		</plugins>
	</build>

	<!-- Links to the Cytoscape Maven repositories. -->
	<repositories>
		<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>
		<repository>
			<id>apache-repo-releases</id>
			<url>https://repository.apache.org/content/repositories/</url>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
	</repositories>

	<dependencies>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>model-api</artifactId>
			<version>${cytoscape.api.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>swing-application-api</artifactId>
			<version>${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.cytoscape</groupId>
			<artifactId>core-task-api</artifactId>
			<version>${cytoscape.api.version}</version>
		</dependency>
		<dependency>
			<groupId>org.ops4j.pax.logging</groupId>
			<artifactId>pax-logging-api</artifactId>
			<version>1.5.2</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.osgi</groupId>
			<artifactId>org.osgi.core</artifactId>
			<version>${osgi.api.version}</version>
		</dependency>
	</dependencies>

</project>