build.gradle example

apply plugin: 'groovy'
apply plugin: 'application'

version = '1.0'

repositories {
    maven  {
        url "http://repo1.maven.org/maven2"
    }
}

sourceSets {
    main {
        groovy {
          srcDir 'src/groovy'
        }
        resources {
          srcDir 'src/resources'
        }
    }
}

dependencies {
    compile group: 'org.codehaus.groovy', name: 'groovy-all', version: '2.4.6'
    compile group: 'commons-cli', name: 'commons-cli', version: '1.3.1'
}

task uberjar(type: Jar, dependsOn:[':compileJava', ':compileGroovy', ':processResources']) {
    from files(sourceSets.main.output.classesDir)
    from configurations.runtime.asFileTree.files.collect { zipTree(it) }

    manifest {
        attributes 'Main-Class': 'SomeClass'
    }
}