assembly.xml

<assembly>

    <id>assembly-pride-proteomes</id>

    <formats>
        <format>zip</format>
    </formats>

    <includeBaseDirectory>false</includeBaseDirectory>

    <dependencySets>
        <dependencySet>
            <!--<outputDirectory>${assembly.dir}/lib</outputDirectory>-->
            <outputDirectory>lib</outputDirectory>
            <unpack>false</unpack>
            <scope>runtime</scope>
        </dependencySet>
    </dependencySets>

    <fileSets>
        <fileSet>
            <directory>${project.basedir}/target</directory>
            <includes>
                <include>*.jar</include>
            </includes>
            <!--<outputDirectory>${assembly.dir}</outputDirectory>-->
            <outputDirectory>/</outputDirectory>
        </fileSet>
        <fileSet>
            <directory>${project.basedir}</directory>
            <outputDirectory>log</outputDirectory>
            <excludes>
                <exclude>**/*</exclude>
            </excludes>
        </fileSet>
        <fileSet>
            <directory>${project.basedir}/script</directory>
            <!--<outputDirectory>${assembly.dir}</outputDirectory>-->
            <outputDirectory>/</outputDirectory>
            <filtered>true</filtered>
        </fileSet>
    </fileSets>
</assembly>