CrossLinX/pom.xml at master · aalhossary/CrossLinX · GitHub

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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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<artifactId>corsslinx</artifactId>
	<version>0.8.0</version>
	<properties>
		<biojava.version>7.2.6</biojava.version>
		<!-- Jmol 16.4.1 plus our thread-safety patch; see jmol-patch/README.md -->
		<jmol.version>16.4.1-threadsafe-1</jmol.version>
	</properties>
	<repositories>
		<repository>
			<id>local-maven-repo</id>
			<url>file:///${project.basedir}/local-maven-repo</url>
		</repository>
	</repositories>
	<build>
		<finalName>crosslinx</finalName>
		<sourceDirectory>src</sourceDirectory>
		<resources>
			<resource>
				<directory>res</directory>
				<filtering>true</filtering>
			</resource>
		</resources>
		<plugins>
			<plugin>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.8.1</version>
				<configuration>
					<!-- BioJava 7 and ciftools-java 7 are compiled for Java 11,
					     so the release target cannot stay at 8: the jar would
					     claim a compatibility it does not have. -->
					<release>11</release>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<configuration>
					<archive>
						<manifest>
							<mainClass>amralhossary.bonds.ProteinParser</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
					<appendAssemblyId>false</appendAssemblyId> <!-- exclude jar-with-dependencies from jar name  -->
				</configuration>
			</plugin>
		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>org.apache.maven</groupId>
			<artifactId>maven-model</artifactId>
			<version>3.3.9</version>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-structure</artifactId>
			<version>${biojava.version}</version>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-structure-gui</artifactId>
			<version>${biojava.version}</version>
			<exclusions>
				<!-- BioJava pins Jmol 14.31.10, the newest on Maven Central
				     (2020). Excluded in favour of the current release below. -->
				<exclusion>
					<groupId>net.sourceforge.jmol</groupId>
					<artifactId>jmol</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<!-- Vendored in local-maven-repo: Jmol is not on Maven Central beyond
		     14.31.10 (2020), and this build additionally carries our
		     thread-safety patch, reported upstream as
		     https://sourceforge.net/p/jmol/bugs/640/. Drop the vendored
		     artifact and depend on an official release once the fix ships.
		     jmol-patch/README.md explains how the jar is rebuilt. -->
		<dependency>
			<groupId>net.sourceforge.jmol</groupId>
			<artifactId>jmol</artifactId>
			<version>${jmol.version}</version>
		</dependency>

	<!-- <dependency> <groupId>docopt</groupId> <artifactId>docopt.java</artifactId>
		<version>0.6.0-SNAPSHOT</version> </dependency> -->
	</dependencies>
	<groupId>hossary</groupId>
	<name>Cross Links Explorer</name>
	<description>Cross Links in Protein structures Explorer</description>
	<scm>
		<url>https://github.com/aalhossary/CrossLinX.git</url>
		<developerConnection>Amr ALHOSSARY</developerConnection>
	</scm>
</project>