pom.xml

<?xml version="1.0"?>
<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>eu.isas.peptideshaker</groupId>
    <artifactId>PeptideShaker</artifactId>
    <packaging>jar</packaging>
    <version>1.16.15</version>
    <name>PeptideShaker</name>
    <url>https://github.com/compomics/peptide-shaker</url>
    <description>Interpretation of proteomics identification results</description>

    <!-- Licence -->
    <licenses>
        <license>
            <name>The Apache Software License, Version 2.0</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0</url>
        </license>
    </licenses>

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

    <!-- Developers -->
    <developers>
        <developer>
            <name>Marc Vaudel</name>
            <id>marc</id>
            <email>marc.vaudel AT uib.no</email>
            <organization>University of Bergen, Norway</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Harald Barsnes</name>
            <id>harald</id>
            <email>harald.barsnes AT uib.no</email>
            <organization>University of Bergen, Norway</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
    </developers>


    <!-- Build -->
    <build>

        <!-- Copy the resources required during building -->
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
                <includes>
                    <include>peptide-shaker.properties</include>
                    <include>peptide-shaker-splash.svg</include>
                </includes>
            </resource>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>false</filtering>
                <excludes>
                    <exclude>peptide-shaker.properties</exclude>
                    <exclude>peptide-shaker-splash.svg</exclude>
                </excludes>
            </resource>
        </resources>

        <!-- Extensions -->
        <extensions>
            <extension>
                <groupId>org.apache.maven.wagon</groupId>
                <artifactId>wagon-ssh</artifactId>
                <version>1.0-beta-2</version>
            </extension>
        </extensions>

        <!-- Plugins -->
        <plugins>

            <!-- SVG to PNG converter plugin -->
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <version>1.2.1</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>java</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <argument>-Dmyproperty=myvalue</argument>
                    <argument>-classpath</argument>
                    <!-- automatically creates the classpath using all project dependencies,
                    also adding the project build directory -->
                    <classpath/>
                    <argument>com.compomics.software.SplashScreen</argument>
                    <mainClass>com.compomics.software.SplashScreen</mainClass>
                    <arguments>
                        <argument>${project.build.directory}</argument>
                        <argument>${project.build.directory}/${project.name}-${project.version}</argument>
                        <argument>peptide-shaker-splash</argument>
                    </arguments>
                </configuration>
            </plugin>
            
            <!-- Compiler plugin -->
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.5</version>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                    <showDeprecation>true</showDeprecation>
                    <debug>true</debug>
                </configuration>
            </plugin>

            <!-- Jar plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <archive>
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                            <mainClass>eu.isas.peptideshaker.PeptideShakerZipFileChecker</mainClass>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib</classpathPrefix>
                            <useUniqueVersions>false</useUniqueVersions>
                        </manifest>
                    </archive>
                    <outputDirectory>${project.build.directory}/${project.name}-${project.version}
                    </outputDirectory>
                </configuration>
            </plugin>

            <!-- Dependency plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>
                                ${project.build.directory}/${project.name}-${project.version}/lib
                            </outputDirectory>
                            <overWriteReleases>true</overWriteReleases>
                            <overWriteSnapshots>true</overWriteSnapshots>
                            <excludeTransitive>false</excludeTransitive>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Resources plugin -->
            <plugin>
                <artifactId>maven-resources-plugin</artifactId>
                <version>2.3</version>
                <executions>
                    <!-- Copy main resources to test resources before testing.  -->
                    <execution>
                        <id>copy-test-resources</id>
                        <phase>generate-test-resources</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <overwrite>true</overwrite>
                            <outputDirectory>src/test/resources</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>src/main/resources</directory>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>

                    <!-- Copy the resources -->
                    <execution>
                        <id>copy-package-resources</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/${project.name}-${project.version}/
                            </outputDirectory>
                            <resources>
                                <resource>
                                    <directory>./</directory>
                                    <includes>
                                        <include>resources/</include>
                                        <include>README.txt</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Create javadoc on build -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.9.1</version>
                <executions>
                    <execution>
                        <id>attach-javadocs</id>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <!-- Pack sources on build -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>2.1.1</version>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <phase>verify</phase>
                        <goals>
                            <goal>jar-no-fork</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            
            <!-- Zip the jar file and the dependencies -->
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <descriptors>
                        <descriptor>src/main/assembly/zip.xml</descriptor>
                    </descriptors>
                    <appendAssemblyId>false</appendAssemblyId>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <!-- this is used for inheritance merges -->
                        <phase>package</phase>
                        <!-- append to the packaging phase. -->
                        <goals>
                            <goal>single</goal>
                            <!-- goals == mojos -->
                        </goals>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>


    <!-- Repositores -->
    <repositories>
        
        <!-- UGent Genesis Maven 2 repository -->
        <repository>
            <id>genesis-maven2-repository</id>
            <name>Genesis maven2 repository</name>
            <url>http://genesis.UGent.be/maven2</url>
            <layout>default</layout>
        </repository>
        
        <!-- old EBI repository -->
        <repository>
            <id>ebi-repo</id> 
            <name>The EBI internal repository</name>
            <url>http://www.ebi.ac.uk/~maven/m2repo</url>
        </repository>

        <!-- EBI repository -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
        
        <!-- EBI SNAPSHOT repo -->
        <repository>
            <id>pst-snapshots</id>
            <name>EBI Nexus Snapshots Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
        </repository>

        <!-- UGent snapshot repository -->
        <repository>
            <id>snapshots</id>
            <name>Archiva Managed Snapshot Repository</name>
            <url>http://genesis.ugent.be/maven/repository/snapshots/</url>
            <releases>
                <enabled>false</enabled>
            </releases>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </repository>

    </repositories>


    <!-- Dependencies -->
    <dependencies>

        <dependency>
            <groupId>com.compomics</groupId>
            <artifactId>utilities</artifactId>
            <version>4.11.19</version>
            <exclusions>
                <exclusion>
                    <artifactId>commons-math</artifactId>
                    <groupId>commons-math</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>servlet-api</artifactId>
                    <groupId>javax.servlet</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>swingx</artifactId>
                    <groupId>org.swinglabs</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>swing-layout</artifactId>
                    <groupId>org.swinglabs</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>sqlite-jdbc</artifactId>
                    <groupId>org.xerial</groupId>
                </exclusion>
            </exclusions>
        </dependency>
        
        <dependency>
            <groupId>de.proteinms.omxparser</groupId>
            <artifactId>omssa-parser</artifactId>
            <version>1.9.0</version>
        </dependency>
        
        <dependency>
            <groupId>de.proteinms.xtandemparser</groupId>
            <artifactId>xtandem-parser</artifactId>
            <version>1.13.0</version>
        </dependency>
        
        <dependency>
            <groupId>com.compomics</groupId>
            <artifactId>mascotdatfile</artifactId>
            <version>3.6.0</version>
            <exclusions>
                <exclusion>
                    <groupId>com.lowagie</groupId>
                    <artifactId>itext</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>3.8.1</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>xpp3</groupId>
            <artifactId>xpp3</artifactId>
            <version>1.1.3.4-RC3</version>
            <type>jar</type>
        </dependency>

        <dependency>
            <groupId>org.swinglabs</groupId>
            <artifactId>swing-layout</artifactId>
            <version>1.0.3</version>
        </dependency>

        <dependency>
            <groupId>jfree</groupId>
            <artifactId>jfreechart</artifactId>
            <version>1.0.13</version>
        </dependency>

        <dependency>
            <groupId>no.uib</groupId>
            <artifactId>jsparklines</artifactId>
            <version>1.0.9</version>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi.jmzml</groupId>
            <artifactId>jmzml</artifactId>
            <version>1.6.8</version>
            <exclusions>
                <exclusion>
                    <artifactId>xxindex</artifactId>
                    <groupId>psidev.psi.tools</groupId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>niklaas</groupId>
            <artifactId>jmol</artifactId>
            <version>12.0.43</version>
            <type>jar</type>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
            <version>2.2</version>
        </dependency>

        <dependency>
            <groupId>no.uib</groupId>
            <artifactId>ols-dialog</artifactId>
            <version>3.4.2</version>
        </dependency>

        <!-- use for adding desktop shortcuts -->
        <dependency>
            <groupId>net.jimmc</groupId>
            <artifactId>jshortcut</artifactId>
            <version>0.4-oberzalek</version>
            <type>jar</type>
        </dependency>
           
        <dependency>   
            <groupId>uk.ac.ebi.pride.jaxb</groupId>   
            <artifactId>pride-jaxb</artifactId>   
            <version>1.0.9</version> 
            <exclusions>
                <exclusion>
                    <artifactId>fastutil</artifactId>
                    <groupId>it.unimi.dsi</groupId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>   
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
            <version>3.1</version>
        </dependency>

        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi</artifactId>
            <version>3.9</version>
        </dependency>

        <!-- can be used to create excel 2007 workbooks -->
        <!--<dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi-ooxml</artifactId>
            <version>3.9</version>
        </dependency>-->

        <dependency>
            <groupId>uk.ac.ebi.pride.archive</groupId>
            <artifactId>web-service-model</artifactId>
            <version>0.2.13</version>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-webmvc</artifactId>
            <version>4.0.4.RELEASE</version>
        </dependency>
 
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
            <version>4.3.3</version>
        </dependency>

        <dependency>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>jackson-mapper-asl</artifactId>
            <version>1.9.13</version>
            <scope>runtime</scope>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi.pride.tools</groupId>
            <artifactId>xmlSchemaValidator</artifactId>
            <version>2.1</version>
        </dependency>

        <!--<dependency>
            <groupId>net.sf.jung</groupId>
            <artifactId>jung2</artifactId>
            <version>2.0.1</version>
            <type>pom</type>                 
        </dependency>-->

        <dependency>
            <groupId>net.sf.jung</groupId>
            <artifactId>jung-graph-impl</artifactId>
            <version>2.0.1</version>
        </dependency>

        <dependency>
            <groupId>net.sf.jung</groupId>
            <artifactId>jung-algorithms</artifactId>
            <version>2.0.1</version>
        </dependency>

        <dependency>
            <groupId>net.sf.jung</groupId>
            <artifactId>jung-visualization</artifactId>
            <version>2.0.1</version>
        </dependency>

    </dependencies>


    <!-- The deployment maven repository-->
    <distributionManagement>
        
        <!-- UGent Genesis archiva repository -->
        <repository>
            <id>archiva.compomics_maven_2</id>
            <name>Internal Release Repository</name>
            <url>http://genesis.ugent.be/archiva/repository/compomics_maven_2</url>
        </repository>
         
        <!-- UGent Genesis archiva snapshot repository -->
        <snapshotRepository>
            <id>archiva.snapshots</id>
            <name>Internal Snapshot Repository</name>
            <url>http://genesis.ugent.be/archiva/repository/snapshots</url>
        </snapshotRepository>
        
    </distributionManagement>

</project>