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pom.xml
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pom.xml
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<?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.reporter</groupId>
<artifactId>Reporter</artifactId>
<packaging>jar</packaging>
<version>0.12.8</version>
<name>Reporter</name>
<url>https://github.com/compomics/reporter</url>
<description>Protein quantification based on reporter ions</description>
<!-- Licence -->
<licenses>
<license>
<name>The Apache Software License, Version 2.0</name>
<url>LICENSE-2.0.txt</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>reporter.properties</include>
<include>reporter-splash.svg</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>reporter.properties</exclude>
<exclude>reporter-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>reporter-splash</argument>
</arguments>
</configuration>
</plugin>
<!-- 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>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
<mainClass>eu.isas.reporter.ReporterZipFileChecker</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>lib</classpathPrefix>
</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>
<configuration>
<source>1.8</source>
</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>
<!-- 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>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>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>5.1.15</version>
<exclusions>
<exclusion>
<artifactId>commons-math</artifactId>
<groupId>commons-math</groupId>
</exclusion>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
<exclusion>
<artifactId>swing-layout</artifactId>
<groupId>org.swinglabs</groupId>
</exclusion>
<exclusion>
<artifactId>batik-all</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>pdf-transcoder</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<groupId>no.uib</groupId>
<artifactId>ols-dialog</artifactId>
</exclusion>
<exclusion>
<groupId>org.swinglabs</groupId>
<artifactId>swingx</artifactId>
</exclusion>
<exclusion>
<artifactId>msv</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>isorelax</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>relaxngDatatype</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>xsdlib</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>jmzidentml</artifactId>
<groupId>uk.ac.ebi.jmzidml</groupId>
</exclusion>
<exclusion>
<artifactId>ssj</artifactId>
<groupId>umontreal.iro.lecuyer.gof</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>eu.isas.peptideshaker</groupId>
<artifactId>PeptideShaker</artifactId>
<version>3.0.9</version>
<exclusions>
<exclusion>
<groupId>de.proteinms.omxparser</groupId>
<artifactId>omssa-parser</artifactId>
</exclusion>
<exclusion>
<groupId>de.proteinms.xtandemparser</groupId>
<artifactId>xtandem-parser</artifactId>
</exclusion>
<exclusion>
<groupId>com.compomics</groupId>
<artifactId>mascotdatfile</artifactId>
</exclusion>
<exclusion>
<groupId>uk.ac.ebi.das</groupId>
<artifactId>jdas</artifactId>
</exclusion>
<exclusion>
<groupId>no.uib</groupId>
<artifactId>ols-dialog</artifactId>
</exclusion>
<exclusion>
<groupId>niklaas</groupId>
<artifactId>jmol</artifactId>
</exclusion>
<exclusion>
<artifactId>twitter4j-core</artifactId>
<groupId>org.twitter4j</groupId>
</exclusion>
<exclusion>
<artifactId>pride-jaxb</artifactId>
<groupId>uk.ac.ebi.pride.jaxb</groupId>
</exclusion>
<exclusion>
<artifactId>charts4j</artifactId>
<groupId>com.googlecode.charts4j</groupId>
</exclusion>
<exclusion>
<artifactId>web-service-model</artifactId>
<groupId>uk.ac.ebi.pride.archive</groupId>
</exclusion>
<exclusion>
<artifactId>xmlSchemaValidator</artifactId>
<groupId>uk.ac.ebi.pride.tools</groupId>
</exclusion>
</exclusions>
</dependency>
<!-- This project depends on the junit JAR file. -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>no.uib</groupId>
<artifactId>jsparklines</artifactId>
<version>1.0.12</version>
</dependency>
<dependency>
<groupId>org.ogce</groupId>
<artifactId>xpp3</artifactId>
<version>1.1.6</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.ujmp</groupId>
<artifactId>ujmp-complete</artifactId>
<version>0.3.0</version>
</dependency>
<dependency>
<groupId>jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.13</version>
</dependency>
<dependency>
<groupId>org.swinglabs</groupId>
<artifactId>swing-layout</artifactId>
<version>1.0.3</version>
</dependency>
<!-- use for adding desktop shortcuts -->
<dependency>
<groupId>net.jimmc</groupId>
<artifactId>jshortcut</artifactId>
<version>0.4-oberzalek</version>
<type>jar</type>
</dependency>
<!-- use for creating excel files -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>5.2.5</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>