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pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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>no.uib</groupId>
<artifactId>PathwayMatcher</artifactId>
<version>1.9.1</version>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
<name>PathwayMatcher</name>
<url>hhttps://github.com/PathwayAnalysisPlatform/PathwayMatcher</url>
<description>Mapping of omics data to reactome pathways.</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>
<!-- Developers -->
<developers>
<developer>
<name>Luis Francisco Hernández Sánchez</name>
<id>francisco</id>
<email>luis.sanchez AT uib.no</email>
<organization>University of Bergen, Norway</organization>
</developer>
<developer>
<name>Marc Vaudel</name>
<id>marc</id>
<email>marc.vaudel AT uib.no</email>
<organization>University of Bergen, Norway</organization>
</developer>
</developers>
<dependencies>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.4.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
<version>5.4.0</version>
<scope>test</scope>
</dependency>
<!-- The CompOmics utilities package -->
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>4.8.9</version>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
<exclusion>
<artifactId>ssj</artifactId>
<groupId>umontreal.iro.lecuyer.gof</groupId>
</exclusion>
<exclusion>
<artifactId>msv</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>relaxngDatatype</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>xsdlib</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>isorelax</artifactId>
<groupId>msv</groupId>
</exclusion>
<exclusion>
<artifactId>xxindex</artifactId>
<groupId>psidev.psi.tools</groupId>
</exclusion>
<exclusion>
<artifactId>ols-dialog</artifactId>
<groupId>no.uib</groupId>
</exclusion>
</exclusions>
<type>jar</type>
</dependency>
<!-- Guava: Google Core Libraries for Java -->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>27.0.1-jre</version>
</dependency>
<!-- Apache Commons Lang -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.8.1</version>
</dependency>
<!-- Apache Commons IO -->
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
</dependency>
<!-- For the probability calculation -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<!-- Apache Http client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.7</version>
<type>jar</type>
</dependency>
<!-- The neo4j driver -->
<dependency>
<groupId>org.neo4j.driver</groupId>
<artifactId>neo4j-java-driver</artifactId>
<version>1.7.2</version>
</dependency>
<!-- Junit extension library for System.exit value testing. -->
<dependency>
<groupId>com.github.stefanbirkner</groupId>
<artifactId>system-rules</artifactId>
<version>1.16.0</version>
<scope>test</scope>
</dependency>
<!-- Picocli: Command line interface -->
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>3.9.5</version>
</dependency>
<!-- Command line parameters library -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
</dependencies>
<repositories>
<!-- UGent Genesis Maven 2 repository -->
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>http://genesis.UGent.be/maven2</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>
<!-- The deployment maven repository. Needed for finding the correct classes of Compomics. -->
<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>