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pom.xml
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pom.xml
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<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>de.mpc.pia</groupId>
<artifactId>pia</artifactId>
<version>1.5.5</version>
<name>PIA - Protein Inference Algorithms</name>
<url>https://github.com/mpc-bioinformatics/pia</url>
<organization>
<url>http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics</url>
<name>Medizinisches Proteom-Center, Medical Bioinformatics</name>
</organization>
<developers>
<developer>
<id>julianu</id>
<name>Julian Uszkoreit</name>
<organization>Medizinisches Proteom-Center, Medical Bioinformatics</organization>
<organizationUrl>http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>Europe/Berlin</timezone>
</developer>
<developer>
<id>ypriverol</id>
<name>Yasset Perez-Riverol</name>
<organization>EMBL-EBI</organization>
<organizationUrl>http://www.ebi.ac.uk</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>Europe/London</timezone>
</developer>
</developers>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<log4j2.version>2.23.1</log4j2.version>
<junit.version>4.13.2</junit.version>
<commons-collections.version>4.4</commons-collections.version>
<commons-text.version>1.12.0</commons-text.version>
<jmzidentml.version>1.2.13</jmzidentml.version>
<jmztab.version>3.0.8</jmztab.version>
<pride-mod.version>2.1.12</pride-mod.version>
<pride-jaxb.version>1.0.22</pride-jaxb.version>
<xxindex.version>0.23</xxindex.version>
<mascotdatfile.version>3.6.1</mascotdatfile.version>
<xtandem-parser.version>1.13.0</xtandem-parser.version>
<compomics-utilities.version>5.1.12</compomics-utilities.version>
<biojava-ontology.version>7.1.1</biojava-ontology.version>
<gson.version>2.11.0</gson.version>
<picocli.version>4.7.6</picocli.version>
<sqlite4java.version>1.0.392</sqlite4java.version>
<sqlite-jdbc.version>3.46.0.0</sqlite-jdbc.version>
<xercesImpl.version>2.12.2</xercesImpl.version>
<!-- override dependencies from some packages to avoid vulnarabilities -->
<logback.version>1.5.6</logback.version>
<jackson-annotations.version>2.17.1</jackson-annotations.version>
<guava.version>33.2.1-jre</guava.version>
<commons-codec.version>1.17.0</commons-codec.version>
<commons-compress.version>1.26.2</commons-compress.version>
<aircompressor.version>0.27</aircompressor.version>
<!-- these are "internal" dependencies, the jar files are delivered together with the source -->
<BaseLib.version>0.0.1-SNAPSHOT</BaseLib.version>
<CvtBaseLib.version>0.0.1-SNAPSHOT</CvtBaseLib.version>
<PDLibrary.version>0.0.1-SNAPSHOT</PDLibrary.version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-jcl</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${commons-text.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>${commons-collections.version}</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>${jmzidentml.version}</version>
</dependency>
<!-- JAXB needs to be added for Java >= 9 -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.1</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.3.9</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>4.0.5</version>
</dependency>
<!-- JAXB additions -->
<!-- pride mod dependency -->
<dependency>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>pride-mod</artifactId>
<version>${pride-mod.version}</version>
</dependency>
<dependency>
<groupId>it.unimi.dsi</groupId>
<artifactId>fastutil</artifactId>
<version>8.5.12</version>
</dependency>
<!-- End pride mod dependency -->
<!-- mzTab dependencies -->
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-model</artifactId>
<version>${jmztab.version}</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-util</artifactId>
<version>${jmztab.version}</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-converters</artifactId>
<version>${jmztab.version}</version>
</dependency>
<!-- End mzTab dependencies-->
<dependency>
<groupId>uk.ac.ebi.pride.jaxb</groupId>
<artifactId>pride-jaxb</artifactId>
<version>${pride-jaxb.version}</version>
</dependency>
<!-- mascotdatfile wants to use a very old version, use newer instead -->
<dependency>
<groupId>psidev.psi.tools</groupId>
<artifactId>xxindex</artifactId>
<version>${xxindex.version}</version>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>mascotdatfile</artifactId>
<version>${mascotdatfile.version}</version>
</dependency>
<dependency>
<groupId>de.proteinms.xtandemparser</groupId>
<artifactId>xtandem-parser</artifactId>
<version>${xtandem-parser.version}</version>
<exclusions>
<!-- these packages break Java 17 dependencies -->
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>${compomics-utilities.version}</version>
<exclusions>
<!-- these packages break Java 17 dependencies -->
<exclusion>
<groupId>org.ogce</groupId>
<artifactId>xpp3</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.axis</groupId>
<artifactId>axis-jaxrpc</artifactId>
</exclusion>
<!-- not needed (only visualization) and highly deprecated -->
<exclusion>
<groupId>umontreal.iro.lecuyer.gof</groupId>
<artifactId>ssj</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-ontology</artifactId>
<version>${biojava-ontology.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson.version}</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>${picocli.version}</version>
</dependency>
<!-- shipped MPC libraries -->
<dependency>
<groupId>de.mpc</groupId>
<artifactId>BaseLib</artifactId>
<version>${BaseLib.version}</version>
</dependency>
<dependency>
<groupId>de.mpc</groupId>
<artifactId>CvtBaseLib</artifactId>
<version>${CvtBaseLib.version}</version>
</dependency>
<dependency>
<groupId>de.mpc</groupId>
<artifactId>PDLibrary</artifactId>
<version>${PDLibrary.version}</version>
</dependency>
<!-- End shipped MPC libraries -->
<!-- SQlite support for MSF files -->
<dependency>
<groupId>com.almworks.sqlite4java</groupId>
<artifactId>sqlite4java</artifactId>
<version>${sqlite4java.version}</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>${sqlite-jdbc.version}</version>
</dependency>
<!-- End SQlite support for MSF files -->
<!-- needed by some testcases and testscenarios -->
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>${xercesImpl.version}</version>
<scope>test</scope>
</dependency>
<!-- override dependencies to avoid vulnarabilities -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson-annotations.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>${commons-compress.version}</version>
</dependency>
<dependency>
<groupId>io.airlift</groupId>
<artifactId>aircompressor</artifactId>
<version>${aircompressor.version}</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.11.0</version>
<configuration>
<release>21</release>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.3.0</version>
<configuration>
<excludes>
<exclude>src/test</exclude>
<exclude>src/test/*.class</exclude>
</excludes>
<archive>
<manifestEntries>
<Add-Opens>java.base/sun.reflect.annotation</Add-Opens>
</manifestEntries>
<index>true</index>
<manifest>
<!-- Adds the classpath to the created manifest -->
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<!-- Configures the main class of the application -->
<mainClass>de.mpc.pia.PIACli</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.6.0</version>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>${project.basedir}/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.11</version>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.2.2</version>
<configuration>
<argLine>${argLine} -Xmx2560m --add-opens java.base/sun.reflect.annotation=ALL-UNNAMED</argLine>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<!-- Nexus EBI repo -->
<repository>
<id>nexus-ebi-release-repo</id>
<name>The EBI Maven 2 Nexus release repository</name>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
</repository>
<repository>
<!-- This repo is required for cpdetector (required by jmzidml->pride-xml-handler->xxindex->cpdetector) and related libraries -->
<!-- This is supplied here because of an HTTP 301 Permanent Redirect on the old URL that xxindex supplies, which breaks fresh builds. -->
<id>sammoa-group</id>
<url>https://nexus.nuiton.org/nexus/content/groups/sammoa-group/</url>
</repository>
<!-- UGent Genesis repository -->
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>https://genesis.ugent.be/maven2</url>
<layout>default</layout>
</repository>
<!-- local files for the PD parser -->
<repository>
<id>pia-shipped-repo</id>
<name>pia-shipped-repo</name>
<releases>
<enabled>true</enabled>
<checksumPolicy>ignore</checksumPolicy>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
<url>file://${project.basedir}/libs</url>
</repository>
</repositories>
</project>