As far as I know You cannot pack other jars into single jar just like that. What You need to do is to extract all the jars and pack the content into single file.
Following piece of code prepares such jar for declared dependencies
apply plugin: 'java'
repositories {
mavenCentral()
}
dependencies {
compile 'com.google.guava:guava:16.0.1'
compile 'com.google.inject:guice:3.0'
}
task fatJar(type: Jar, dependsOn: jar) {
baseName = project.name + '-fat'
deps = configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) }
from(deps) {
exclude 'META-INF/MANIFEST.MF'
}
}