/
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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<packaging>pom</packaging>
<version>3.0.5-SNAPSHOT</version>
<name>biojava</name>
<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.</description>
<url>http://www.biojava.org</url>
<organization>
<name>BioJava</name>
<url>http://www.biojava.org</url>
</organization>
<licenses>
<license>
<name>GNU LGPL v2</name>
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<connection>scm:svn:svn://code.open-bio.org/biojava/biojava-live/trunk</connection>
<developerConnection>scm:svn:svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk</developerConnection>
<url>http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk</url>
</scm>
<repositories>
<repository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Maven 2 Repository</name>
<url>http://download.java.net/maven/2</url>
</repository>
<repository>
<id>maven-repository.dev.java.net</id>
<name>Java.net Maven 1 Repository (legacy)</name>
<url>http://download.java.net/maven/1</url>
<layout>default</layout>
</repository>
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Maven 2 Repository</name>
<url>http://download.java.net/maven/2</url>
</pluginRepository>
<pluginRepository>
<id>maven-repository.dev.java.net</id>
<name>Java.net Maven 1 Repository (legacy)</name>
<url>http://download.java.net/maven/1</url>
<layout>default</layout>
</pluginRepository>
</pluginRepositories>
<distributionManagement>
<downloadUrl>http://www.biojava.org/download/maven/</downloadUrl>
<repository>
<uniqueVersion>false</uniqueVersion>
<id>biojava-maven-repo</id>
<name>BioJava Maven Repository</name>
<url>scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven/</url>
<layout>default</layout>
</repository>
</distributionManagement>
<properties>
<jdk.version>1.6</jdk.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<maxmem>512M</maxmem>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.0</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3</version>
</plugin>
<plugin>
<artifactId>maven-scm-plugin</artifactId>
<version>1.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.5</version>
</plugin>
<plugin>
<groupId>net.sf</groupId>
<artifactId>stat-scm</artifactId>
<version>1.2.0</version>
</plugin>
<plugin>
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
<version>0.7.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.1</version>
<configuration>
<tagBase>svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/tags</tagBase>
<remoteTagging>true</remoteTagging>
<preparationGoals>clean install</preparationGoals>
<autoVersionSubmodules>true</autoVersionSubmodules>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.7</version>
<configuration>
<footer><script src="http://www.google-analytics.com/urchin.js" type="text/javascript"></script><script type="text/javascript">_uacct = "UA-1326640-1";urchinTracker();</script></footer>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.7</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>1.2.2</version>
</dependency>
<dependency>
<groupId>javax.persistence</groupId>
<artifactId>persistence-api</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-jdk1.5</artifactId>
<version>0.7.3</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.4.0</version>
</dependency>
</dependencies>
</dependencyManagement>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.1.2</version>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.7</version>
<configuration>
<aggregate>true</aggregate>
<minmemory>140m</minmemory>
<maxmemory>140m</maxmemory>
<breakiterator>true</breakiterator>
<quiet>true</quiet>
<source>1.6</source>
<verbose>false</verbose>
<linksource>true</linksource>
<!-- <detectLinks>true</detectLinks> -->
<links>
<!-- JSE -->
<link>http://java.sun.com/j2se/1.6.0/docs/api/</link>
<!-- Libraries -->
<!-- <link>http://jakarta.apache.org/commons/collections/apidocs</link>
<link>http://jakarta.apache.org/commons/logging/apidocs/</link> <link>http://www.junit.org/junit/javadoc/</link> -->
<link>http://logging.apache.org/log4j/docs/api/</link>
<link>http://jakarta.apache.org/regexp/apidocs/</link>
<link>http://jakarta.apache.org/velocity/api/</link>
</links>
</configuration>
</plugin>
<plugin>
<groupId>net.sf</groupId>
<artifactId>stat-scm</artifactId>
<version>1.2.0</version>
<configuration>
<includes>
<include>**/*.java</include>
</includes>
<excludes>
<exclude>**/test/**/*.java</exclude>
</excludes>
<tags>3.0</tags>
<tagsDir>/releases/</tagsDir>
<cacheDir>/statsvn/</cacheDir>
<title>BioJava SVN statistics</title>
</configuration>
</plugin>
</plugins>
</reporting>
<modules>
<module>biojava3-core</module>
<module>biojava3-phylo</module>
<module>biojava3-sequencing</module>
<module>biojava3-structure</module>
<module>biojava3-structure-gui</module>
<module>biojava3-genome</module>
<module>biojava3-modfinder</module>
<module>biojava3-alignment</module>
<module>biojava3-ws</module>
<module>biojava3-protein-disorder</module>
<module>biojava3-aa-prop</module>
<module>integrationtest</module>
</modules>
</project>