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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>edu.umn.msi.gx</groupId>
<artifactId>mzToSQLite</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<jmzidentml.version>1.1.4-SNAPSHOT</jmzidentml.version>
<pride.jaxb.version>1.0.8</pride.jaxb.version>
<pride.utilities.version>0.1.21</pride.utilities.version>
<apache.commons.net.version>3.0.1</apache.commons.net.version>
<apache.http.client>4.2.1</apache.http.client>
<java.mail.version>1.4.4</java.mail.version>
<java.webstart.version>1.5.0</java.webstart.version>
<java.help.version>2.0.02</java.help.version>
<assembly.dir>${name}-${version}</assembly.dir>
</properties>
<repositories>
<repository>
<id>tmate</id>
<url>http://maven.tmatesoft.com/content/repositories/releases</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>1.6.8</version>
<exclusions>
<exclusion>
<artifactId>xxindex</artifactId>
<groupId>psidev.psi.tools</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>1.1.10-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.mzgraph</groupId>
<artifactId>pride-mzgraph-browser</artifactId>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>jmzreader</artifactId>
<version>1.2.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>pkl-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>dta-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>ms2-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mgf-parser</artifactId>
<version>1.2.4</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzxml-parser</artifactId>
<version>1.3.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzdata-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzml-wrapper</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>pride-wrapper</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.130</version>
</dependency>
<dependency>
<groupId>org.tmatesoft.sqljet</groupId>
<artifactId>sqljet</artifactId>
<version>1.1.10</version>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>3.47.2</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>batik-all</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>pdf-transcoder</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>jfreechart</artifactId>
<groupId>jfree</groupId>
</exclusion>
<exclusion>
<artifactId>xercesImpl</artifactId>
<groupId>xerces</groupId>
</exclusion>
<exclusion>
<artifactId>ssj</artifactId>
<groupId>umontreal.iro.lecuyer.gof</groupId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>edu.umn.msi.gx.mztosqlite.MzToSQLite</mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>