File: pom.xml

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<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">
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>4.2.12</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<artifactId>biojava-aa-prop</artifactId>
	<name>biojava-aa-prop</name>
	<url>http://www.biojava.org</url>

	<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>

	<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-assembly-plugin</artifactId>
				<configuration>
					<finalName>AAProperties</finalName>
					<archive>
						<manifest>
							<addClasspath>true</addClasspath>
							<mainClass>org.biojava.nbio.aaproperties.CommandPrompt</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
					<fileSets>
						<fileSet>
							<!-- TODO: use expresssions instead: ${project.build.sourceDirectory}, 
								etc -->
							<directory>${project.basedir}/src</directory>
							<useDefaultExcludes>true</useDefaultExcludes>
						</fileSet>
					</fileSets>
				</configuration>
				<executions>
					<execution>
						<id>make-assembly</id> <!-- this is used for inheritance merges -->
						<phase>package</phase> <!-- bind to the packaging phase -->
						<goals>
							<goal>single</goal>
						</goals>
					</execution>
				</executions>
			</plugin>
		</plugins>
	</build>

	<dependencies>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>4.2.12</version>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-structure</artifactId>
			<version>4.2.12</version>
		</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>			

				
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
	</dependencies>
</project>