pom.xml

<?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>org.mskcc.cbio.paralyzer</groupId>
	<artifactId>peralyzer</artifactId>
	<packaging>war</packaging>
	<version>1.0-SNAPSHOT</version>
	<name>Peralyzer</name>
	<!--url>http://cbio.mskcc.org/pcviz</url-->

	<properties>
		<java.version>1.7</java.version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<slf4j.version>1.6.4</slf4j.version>
		<spring.version>3.1.0.RELEASE</spring.version>
	</properties>

	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<artifactId>maven-compiler-plugin</artifactId>
					<configuration>
						<source>1.7</source>
						<target>1.7</target>
					</configuration>
				</plugin>
			</plugins>
		</pluginManagement>
		<plugins>
			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>tomcat-maven-plugin</artifactId>
				<version>1.1</version>
				<configuration>
					<url>http://localhost:8080/manager/text</url>
					<server>localhost</server>
				</configuration>
			</plugin>
		</plugins>
		<!-- prevent some resources from getting into war -->
		<resources>
			<resource>
				<directory>src/main/resources</directory>
				<excludes>
					<exclude>histogram_data/**</exclude>
					<exclude>matrix_data/**</exclude>
					<exclude>network_models/**</exclude>
				</excludes>
			</resource>
		</resources>
	</build>

	<dependencies>
		<!-- javax servlet -->
		<dependency>
			<groupId>javax.servlet</groupId>
			<artifactId>servlet-api</artifactId>
			<version>2.3</version>
			<scope>provided</scope>
		</dependency>

		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-io</artifactId>
			<version>1.3.2</version>
		</dependency>

		<dependency>
			<groupId>commons-fileupload</groupId>
			<artifactId>commons-fileupload</artifactId>
			<version>1.2.2</version>
		</dependency>

		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.7</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>log4j</groupId>
			<artifactId>log4j</artifactId>
			<version>1.2.16</version>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>${slf4j.version}</version>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>jcl-over-slf4j</artifactId>
			<version>${slf4j.version}</version>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-log4j12</artifactId>
			<version>${slf4j.version}</version>
		</dependency>


		<!-- Spring 3 dependencies -->
		<dependency>
			<groupId>org.springframework</groupId>
			<artifactId>spring-core</artifactId>
			<version>${spring.version}</version>
		</dependency>

		<dependency>
			<groupId>org.springframework</groupId>
			<artifactId>spring-web</artifactId>
			<version>${spring.version}</version>
		</dependency>

		<dependency>
			<groupId>org.springframework</groupId>
			<artifactId>spring-webmvc</artifactId>
			<version>${spring.version}</version>
		</dependency>

		<dependency>
			<groupId>net.sf.flexjson</groupId>
			<artifactId>flexjson</artifactId>
			<version>2.1</version>
		</dependency>

		<!-- ehcache -->
		<dependency>
			<groupId>net.sf.ehcache</groupId>
			<artifactId>ehcache-core</artifactId>
			<version>2.5.1</version>
		</dependency>

		<!-- AOP dependency -->
		<dependency>
			<groupId>cglib</groupId>
			<artifactId>cglib</artifactId>
			<version>2.2</version>
		</dependency>

		<!-- R -->
		<!--dependency>
			<groupId>org.nuiton.thirdparty</groupId>
			<artifactId>Rserve</artifactId>
			<version>1.7-3</version>
		</dependency>

		<dependency>
			<groupId>org.nuiton.thirdparty</groupId>
			<artifactId>REngine</artifactId>
			<version>1.7-3</version>
		</dependency-->

	</dependencies>
</project>