/
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>PDV</groupId>
<artifactId>PDV</artifactId>
<packaging>jar</packaging>
<version>2.1.0-beta</version>
<name>PDV</name>
<url>https://github.com/wenbostar/PDV</url>
<description>An integrative proteomics viewer</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>
<!-- Build -->
<build>
<!-- 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>3.8.1</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>PDVGUI.gui.PDVMainClass</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>
<version>3.2.0</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>
${project.build.directory}/${project.name}-${project.version}/lib
</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<excludeTransitive>false</excludeTransitive>
</configuration>
</execution>
</executions>
</plugin>
<!-- Resources plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>copy-package-resources</id>
<phase>package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${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>
</plugins>
</build>
<!-- Repositores -->
<repositories>
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>https://genesis.UGent.be/maven2</url>
<layout>default</layout>
</repository>
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>https://www.ebi.ac.uk/~maven/m2repo</url>
</repository>
<repository>
<id>pst-release</id>
<name>EBI Nexus Repository</name>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
</repository>
<repository>
<id>pst-snapshots</id>
<name>EBI Nexus Snapshots Repository</name>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
</repository>
<repository>
<id>snapshots</id>
<name>Archiva Managed Snapshot Repository</name>
<url>https://genesis.ugent.be/maven/repository/snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>nexus-ebi-release-repo</id>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
</repository>
</repositories>
<!-- Dependencies -->
<dependencies>
<dependency>
<groupId>com.github.chhh</groupId>
<artifactId>msftbx</artifactId>
<version>1.8.8</version>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>4.11.14</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>com.compomics</groupId>
<artifactId>mascotdatfile</artifactId>
<version>3.6.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.swinglabs</groupId>
<artifactId>swing-layout</artifactId>
<version>1.0.3</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>3.0.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.jaxb</groupId>
<artifactId>pride-jaxb</artifactId>
<version>1.0.22</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung-visualization</artifactId>
<version>2.1.1</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.45.2.0</version>
</dependency>
<dependency>
<groupId>com.twelvemonkeys.imageio</groupId>
<artifactId>imageio-tiff</artifactId>
<version>3.4.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>pride-mod</artifactId>
<version>2.1.12</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.jgoodies</groupId>
<artifactId>jgoodies-forms</artifactId>
<version>1.9.0</version>
</dependency>
<dependency>
<groupId>io.github.msdk</groupId>
<artifactId>msdk-datamodel</artifactId>
<version>0.0.16</version>
</dependency>
<dependency>
<groupId>io.github.msdk</groupId>
<artifactId>msdk-io-mzml</artifactId>
<version>0.0.16</version>
</dependency>
<dependency>
<groupId>io.github.msdk</groupId>
<artifactId>msdk-io-mzxml</artifactId>
<version>0.0.16</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.5</version>
</dependency>
<dependency>
<groupId>org.reactome.server.tools</groupId>
<artifactId>analysis-core</artifactId>
<version>3.3.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.json/json -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20240303</version>
</dependency>
</dependencies>
<!--The deployment maven repository-->
<distributionManagement>
<repository>
<id>archiva.compomics_maven_2</id>
<name>Internal Release Repository</name>
<url>https://genesis.ugent.be/archiva/repository/compomics_maven_2</url>
</repository>
<snapshotRepository>
<id>archiva.snapshots</id>
<name>Internal Snapshot Repository</name>
<url>https://genesis.ugent.be/archiva/repository/snapshots</url>
</snapshotRepository>
</distributionManagement>
</project>