<?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">
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>4.2.8</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<artifactId>biojava-genome</artifactId>
	<name>biojava-genome</name>

	<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>

	<repositories>
		<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>
	<url>http://maven.apache.org</url>
	<build>
		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>
		
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>

				<configuration>
					<debug>true</debug>
				</configuration>
			</plugin>

			<plugin>
				<artifactId>maven-clean-plugin</artifactId>
				<configuration>
					<filesets>
						<fileset>
							<directory>${basedir}/src/test/resources/testoutput</directory>
							<includes>
								<include>**/volvox_all.faa</include>
							</includes>
						</fileset>
					</filesets>
				</configuration>
			</plugin>

		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<scope>compile</scope>
			<version>19.0</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>4.2.8</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-alignment</artifactId>
			<version>4.2.8</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>junit-addons</groupId>
			<artifactId>junit-addons</artifactId>
			<version>1.4</version>
			<scope>test</scope>
			<exclusions>
				<exclusion>
					<groupId>xerces</groupId>
					<artifactId>xmlParserAPIs</artifactId>
				</exclusion>
				<exclusion>
					<groupId>xerces</groupId>
					<artifactId>xercesImpl</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
		<dependency>
        	<groupId>org.slf4j</groupId>
        	<artifactId>slf4j-api</artifactId>
    	</dependency>
    	<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-slf4j-impl</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-api</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-core</artifactId>
  		</dependency>			
	</dependencies>

</project>

