Using Gradle to build a jar with dependencies

The answer by @felix almost brought me there. I had two issues:

1. With Gradle 1.5, the manifest tag was not recognised inside the fatJar task, so the Main-Class attribute could not directly be set
2. the jar had conflicting external META-INF files.

The following setup resolves this

jar {
  manifest {
    attributes(
      'Main-Class': 'my.project.main',
    )
  }
}

task fatJar(type: Jar) {
  manifest.from jar.manifest
  classifier = 'all'
  from {
    configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
  } {
    exclude "META-INF/*.SF"
    exclude "META-INF/*.DSA"
    exclude "META-INF/*.RSA"
  }
  with jar
}

To add this to the standard assemble or build task, add:

artifacts {
    archives fatJar
}

Edit: thanks to @mjaggard: in recent versions of Gradle, change configurations.runtime to configurations.runtimeClasspath

I posted a solution in JIRA against Gradle:

// Include dependent libraries in archive.
mainClassName = "com.company.application.Main"

jar {
  manifest { 
    attributes "Main-Class": "$mainClassName"
  }  

  from {
    configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
  }
}

Note that mainClassName must appear BEFORE jar {.