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>com.compomics</groupId>
    <artifactId>utilities</artifactId>
    <packaging>jar</packaging>
    <version>5.1.12</version>
    <name>computational omics utilities</name>
    <url>https://github.com/compomics/compomics-utilities</url>
    <description>Open source java library for computational proteomics</description>


    <!-- Set the version number for the whole project -->
    <properties>
        <logging.file.path.name>compomics-utilities-log4j.log</logging.file.path.name>
        <logging.file.max.size>5000KB</logging.file.max.size>
        <logging.pattern>[%d{dd-MMM-yyyy HH:mm:ss} - %p]  "%m"   (%C:%L)%n</logging.pattern>
        <logging.level.default>DEBUG</logging.level.default>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
    </properties>


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


    <!-- Developers -->
    <developers>
        <developer>
            <name>Lennart Martens</name>
            <id>lennart</id>
            <email>lennart.martens AT UGent.be</email>
            <organization>Ghent University and FWO Vlaanderen</organization>
            <roles>
                <role>UML Model Design</role>
                <role>Java Developer</role>
                <role>Documentation</role>
            </roles>
        </developer>
        <developer>
            <name>Harald Barsnes</name>
            <id>harald</id>
            <email>harald.barsnes AT uib.no</email>
            <organization>University of Bergen</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Marc Vaudel</name>
            <id>marc</id>
            <email>marc.vaudel AT uib.no</email>
            <organization>University of Bergen</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Kenny Helsens</name>
            <id>kenny</id>
            <email>kenny.helsens AT UGent.be</email>
            <organization>University of Ghent</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Kenneth Verheggen</name>
            <id>kenneth</id>
            <email>kenneth.verheggen AT UGent.be</email>
            <organization>University of Ghent</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Niklaas Colaert</name>
            <id>kenny</id>
            <email>niklaas.colaert AT UGent.be</email>
            <organization>University of Ghent</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Dominik Kopczynski</name>
            <id>dominik</id>
            <email>dominik.kopczynski AT isas.de</email>
            <organization>Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Carlos Horro</name>
            <id>carlos</id>
            <email>carlos.horro AT uib.no</email>
            <organization>University of Bergen</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Dafni Skiadopoulou</name>
            <id>dafni</id>
            <email>Dafni Skiadopoulou AT uib.no</email>
            <organization>University of Bergen</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>compomics-utilities.properties</include>
                </includes>
            </resource>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>false</filtering>
                <excludes>
                    <exclude>compomics-utilities.properties</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>

            <!-- Compiler plugin -->
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.5</version>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</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>
                            <mainClass>com.compomics.util.examples.UtilitiesDemo</mainClass>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib</classpathPrefix>
                        </manifest>
                    </archive>
                    <outputDirectory>${project.build.directory}/${project.artifactId}-${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.artifactId}-${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>
                <!-- Copy resources into appropriate folder upon packaging -->
                <executions>
                    
                    <!-- Copy the classes -->
                    <execution>
                        <id>copy-resources2</id>
                        <phase>compile</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <overwrite>true</overwrite>
                            <outputDirectory>target/classes</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>src/main/resources</directory>
                                    <filtering>true</filtering>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                    
                
        
                    
                    <!-- Copy main resources into test classpath when running the tests -->
                    <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-resources</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>./</directory>
                                    <includes>
                                        <include>resources/</include>
                                        <include>exampleFiles/</include>
                                        <include>compomics-utilities.ico</include>
                                        <include>LICENSE-2.0.txt</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>
                <configuration>
                    <source>1.8</source>
                    <destDir>docs/javadoc</destDir>
                    <notimestamp>true</notimestamp>
                    <locale>en</locale>
                </configuration>
                <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>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-deploy-plugin</artifactId>
                <version>2.7</version>
            </plugin>

            <!-- Deploy the JavaDoc on build -->
            <!--<plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>wagon-maven-plugin</artifactId>
                <version>1.0-beta-5</version>
                <executions>
                    <execution>
                        <id>upload-javadoc</id>
                        <phase>deploy</phase>
                        <goals>
                            <goal>upload</goal>
                        </goals>
                        <configuration>
                            <fromDir>${project.build.directory}/apidocs</fromDir>
                            <include>*</include>
                            <serverId>genesis-maven2-repo</serverId>
                            <url>scp://genesis.ugent.be/</url>
                            <toDir>/home/maven/public_html/maven2/com/compomics/utilities/javadoc/</toDir>
                        </configuration>
                    </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>


    <!-- Repositories -->
    <repositories>
 
        <!-- UGent Genesis repository -->
        <repository>
            <id>genesis-maven2-repository</id>
            <name>Genesis maven2 repository</name>
            <url>https://genesis.ugent.be/archiva/repository/maven2/</url>
            <layout>default</layout>
        </repository>
        
        <!-- EBI internal repository -->
        <repository>
            <id>ebi-repo</id> 
            <name>The EBI internal repository</name>
            <url>https://www.ebi.ac.uk/~maven/m2repo</url>
        </repository>

        <!-- EBI repository -->
        <repository>
            <id>nexus-ebi-release-repo</id>
            <name>EBI Nexus Repository</name>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
        </repository>
        
        <!-- EBI SNAPSHOT repo -->
        <repository>
            <id>nexus-ebi-snapshot-repo</id>
            <name>EBI Nexus Snapshots Repository</name>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
        </repository>

    </repositories>


    <!-- Dependencies -->
    <dependencies>
        <!-- This project depends on the junit JAR file.-->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.13.2</version>
            <scope>test</scope>
            <type>jar</type>
        </dependency>

        <!-- The Servlet API from Sun -->
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
            <version>2.5</version>
        </dependency>
        
        <dependency>
            <groupId>javax.xml.bind</groupId>
            <artifactId>jaxb-api</artifactId>
            <version>2.3.1</version>
        </dependency>
        
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.16.1</version>
        </dependency>
        
        <dependency>
            <groupId>org.xerial</groupId>
            <artifactId>sqlite-jdbc</artifactId>
            <version>3.45.2.0</version>
        </dependency>

        <!-- The log4j logging framework -->
        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-api</artifactId>
            <version>2.23.1</version>
        </dependency>

        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-core</artifactId>
            <version>2.23.1</version>
        </dependency>
        
        <dependency>
            <groupId>org.ogce</groupId>
            <artifactId>xpp3</artifactId>
            <version>1.1.6</version>
            <type>jar</type>
        </dependency>

        <!-- This project depends on jgoodies looks -->
        <dependency>
            <groupId>com.jgoodies</groupId>
            <artifactId>looks</artifactId>
            <version>2.2.2</version>
        </dependency>

        <!-- Required by the user interface -->
        <dependency>
            <groupId>org.swinglabs</groupId>
            <artifactId>swing-layout</artifactId>
            <version>1.0.3</version>
            <scope>compile</scope>
        </dependency>
        
        <!-- Suffix array construction -->
        <dependency>
            <groupId>com.carrotsearch</groupId>
            <artifactId>jsuffixarrays</artifactId>
            <version>0.1.0</version>
        </dependency>

        <dependency>
            <groupId>org.swinglabs</groupId>
            <artifactId>swingx</artifactId>
            <version>0.9.1</version>
            <exclusions>
                <exclusion>
                    <artifactId>swing-worker</artifactId>
                    <groupId>org.swinglabs</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>multiplegradientpaint</artifactId>
                    <groupId>org.swinglabs</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>filters</artifactId>
                    <groupId>com.jhlabs</groupId>
                </exclusion>
            </exclusions>
        </dependency>

        <!-- Used for exporting to svg, png, gif etc.-->
        <dependency>
            <groupId>batik</groupId>
            <artifactId>batik-all</artifactId>
            <version>1.6</version>
            <type>jar</type>
        </dependency>
        <dependency>
            <groupId>batik</groupId>
            <artifactId>pdf-transcoder</artifactId>
            <version>1.0</version>
            <type>jar</type>
        </dependency>

        <dependency>
            <groupId>xerces</groupId>
            <artifactId>xercesImpl</artifactId>
            <version>2.12.2</version>
        </dependency>
        
        <dependency>
            <groupId>jakarta.xml.bind</groupId>
            <artifactId>jakarta.xml.bind-api</artifactId>
            <version>4.0.2</version>
        </dependency>

        <dependency>
            <groupId>psidev.psi.tools</groupId>
            <artifactId>xxindex</artifactId>
            <version>0.23</version>
        </dependency>

        <dependency>
            <groupId>jfree</groupId>
            <artifactId>jfreechart</artifactId>
            <version>1.0.13</version>
        </dependency>
        
        <dependency>
            <groupId>no.uib</groupId>
            <artifactId>jsparklines</artifactId>
            <version>1.0.12</version>
        </dependency>
        
        <dependency>
            <groupId>no.uib</groupId>
            <artifactId>ols-dialog</artifactId>
            <version>3.4.0</version>
        </dependency>
  
        <!-- Apache Commons - Command Line Interface -->
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.6.0</version>
        </dependency>

        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
            <version>3.10.0</version>
        </dependency>

        <dependency>
            <groupId>commons-httpclient</groupId>
            <artifactId>commons-httpclient</artifactId>
            <version>3.1</version>
            <type>jar</type>
        </dependency>
        
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-compress</artifactId>
            <version>1.26.1</version>
        </dependency>

        <dependency>   
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-text</artifactId>
            <version>1.11.0</version>
        </dependency>

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

        <dependency>
            <groupId>uk.ac.ebi.pride.tools</groupId>
            <artifactId>braf</artifactId>
            <version>1.0.1</version>
        </dependency>
        
        <dependency>
            <groupId>uk.ac.ebi.pride.archive</groupId>
            <artifactId>web-service-model</artifactId>
            <version>0.2.12</version>
        </dependency> 
        
        <dependency>
            <groupId>umontreal.iro.lecuyer.gof</groupId>
            <artifactId>ssj</artifactId>
            <version>2.5.0</version>
            <type>jar</type>
        </dependency>
        
        <!-- Used for PRIDE XML schema validation.-->
        <dependency>
            <groupId>msv</groupId>
            <artifactId>msv</artifactId>
            <version>20050913</version>
        </dependency>
        <dependency>
            <groupId>msv</groupId>
            <artifactId>isorelax</artifactId>
            <version>20050913</version>
        </dependency>
        <dependency>
            <groupId>msv</groupId>
            <artifactId>relaxngDatatype</artifactId>
            <version>20050913</version>
        </dependency>
        <dependency>
            <groupId>msv</groupId>
            <artifactId>xsdlib</artifactId>
            <version>20050913</version>
        </dependency>

        <dependency>
            <groupId>net.jimmc</groupId>
            <artifactId>jshortcut</artifactId>
            <version>0.4-oberzalek</version>
            <type>jar</type>
        </dependency>
        
        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi</artifactId>
            <version>5.2.5</version>
        </dependency>
        
        <!-- can be used to create xlsx workbooks supporting more than 65,535 lines -->
        <!--<dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi-ooxml</artifactId>
            <version>4.1.1</version>
        </dependency>-->
        
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
            <version>2.10.1</version>
            <type>jar</type>
        </dependency>
        
        <dependency>
            <groupId>io.airlift</groupId>
            <artifactId>aircompressor</artifactId>
            <version>0.26</version>
            <type>jar</type>
        </dependency>
        
        <!-- Graph library for the PTM localization -->
        <dependency>
            <groupId>org.jgrapht</groupId>
            <artifactId>jgrapht-core</artifactId>
            <version>1.5.2</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>https://genesis.ugent.be/archiva/repository/maven2/</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>