pom.xml

<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>hk.ust.bioinformatics</groupId>
    <artifactId>ECL</artifactId>
    <version>1.1.2</version>
    <packaging>jar</packaging>

    <name>ECL</name>
    <description>A fast and exhaustive cross-linked peptides identification tool.</description>
    <url>https://github.com/fcyu/ECL</url>
    <licenses>
        <license>
            <name>Apache 2</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
        </license>
    </licenses>
    <organization>
        <name>Laboratory for Bioinformatics and Computational Biology, HKUST</name>
        <url>http://bioinformatics.ust.hk/</url>
    </organization>
    <developers>
        <developer>
            <id>FYu</id>
            <name>Fengchao Yu</name>
            <email>fyuab@connect.ust.hk</email>
            <organization>BME, HKUST</organization>
        </developer>
    </developers>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <maven.compiler.source>1.7</maven.compiler.source>
        <maven.compiler.target>1.7</maven.compiler.target>
    </properties>

    <dependencies>
        <dependency>
            <groupId>uk.ac.ebi.pride.tools</groupId>
            <artifactId>jmzreader</artifactId>
            <version>2.0.7</version>
            <type>jar</type>
        </dependency>
        <dependency>
            <groupId>uk.ac.ebi.pride.tools</groupId>
            <artifactId>mzxml-parser</artifactId>
            <version>1.3.9</version>
            <type>jar</type>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-core</artifactId>
            <version>1.4.14</version>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <version>1.4.14</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>2.0.9</version>
        </dependency>
    </dependencies>

    <repositories>
        <!-- EBI repo -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
    </repositories>

    <build>
        <plugins>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                    <archive>
                        <manifest>
                            <mainClass>proteomics.SearchMain</mainClass>
                        </manifest>
                    </archive>
                    <appendAssemblyId>
                        false
                    </appendAssemblyId>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>