pom-local.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>uk.ac.ebi.rdt</groupId>
    <artifactId>rdt</artifactId>
    <description>Reaction Decoder Tool</description>
    <version>2.6.0</version>
    <packaging>jar</packaging>
    <properties>
        <jdk.version>11</jdk.version>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <maven.compiler.source>11</maven.compiler.source>
        <maven.compiler.target>11</maven.compiler.target>
        <mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
    </properties>
   
    <licenses>
        <license>
            <name>GNU General Lesser Public License (LGPL) version 3.0</name>
            <url>https://www.gnu.org/licenses/lgpl-3.0.en.html</url>
        </license>
    </licenses>
    <!--<prerequisites>
        <maven>3.0</maven>
    </prerequisites>-->

    <dependencies>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.13</version>
            <scope>test</scope>
        </dependency>
        
        <dependency>
            <groupId>org.jgrapht</groupId>
            <artifactId>jgrapht-core</artifactId>
            <version>1.4.0</version>
        </dependency>
        
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-bundle</artifactId>
            <version>2.4-SNAPSHOT</version>
        </dependency>
        
        <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.4</version>
        </dependency>
        
        <dependency>
            <groupId>org.apache.directory.studio</groupId>
            <artifactId>org.apache.commons.io</artifactId>
            <version>2.4</version>
        </dependency>
       
    </dependencies>
    
    <build>
        <plugins>
            <!-- download source code in Eclipse, best practice -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-eclipse-plugin</artifactId>
                <version>2.10</version>
                <configuration>
                    <downloadSources>true</downloadSources>
                    <downloadJavadocs>false</downloadJavadocs>
                </configuration>
            </plugin>

            <!-- Set a compiler level -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.8.1</version>
                <configuration>
                    <source>${jdk.version}</source>
                    <target>${jdk.version}</target>
                    <showDeprecation>true</showDeprecation>
                </configuration>
            </plugin>

            <!-- Maven Assembly Plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>3.3.0</version>
                <configuration>
                    <!-- get all project dependencies -->
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                    <!-- MainClass in mainfest make a executable jar -->
                    <archive>
                        <manifest>
                            <mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
                        </manifest>
                    </archive>

                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <!-- bind to the packaging phase -->
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>
    <name>Reaction Decoder Tool</name>  
</project>