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>
    <groupId>net.rguha</groupId>
    <artifactId>cdkdescui</artifactId>
    <packaging>jar</packaging>
    <version>1.4.7</version>
    <name>cdkdescui</name>
    <url>http://maven.apache.org</url>


    <repositories>
        <!--<repository>-->
            <!--<id>java.net</id>-->
            <!--<url>http://download.java.net/maven/2</url>-->
        <!--</repository>-->
        <repository>
            <id>MavenCentral</id>
            <name>Maven repository</name>
            <url>http://repo1.maven.org/maven2</url>
            <releases>
                <enabled>true</enabled>
            </releases>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
        <repository>
            <id>ebi-repo</id>
            <url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
        <repository>
            <id>ebi-repo-snapshots</id>
            <url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/</url>
            <releases>
                <enabled>false</enabled>
            </releases>
        </repository>
        <repository>
            <id>repo</id>
            <url>file://${basedir}/local.repo</url>
        </repository>
    </repositories>

    <dependencies>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.0</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>1.6.1</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-jdk14</artifactId>
            <version>1.6.1</version>
        </dependency>

        <dependency>
            <groupId>checkboxtree</groupId>
            <artifactId>checkboxtree</artifactId>
            <version>0.1</version>
        </dependency>

        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-fingerprint</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-qsarmolecular</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-silent</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-signature</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-data</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-standard</artifactId>
            <version>2.0</version>
        </dependency>

    </dependencies>

    <build>
        <plugins>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                </configuration>
            </plugin>


            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.2</version>
                <configuration>
                    <finalName>CDKDescUI-${project.version}</finalName>
                    <transformers>
                        <transformer
                                implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <mainClass>net.guha.apps.cdkdesc.CDKdesc</mainClass>
                        </transformer>
                    </transformers>
                    <filters>
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>


            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <descriptorRefs>
                        <descriptorRef>src</descriptorRef>
                    </descriptorRefs>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                        <configuration>
                            <finalName>CDKDescUI-${project.version}</finalName>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>


</project>