In that case I would suggest laying your project out as a minimal Groovy 
project

   rootDir -- src -- main -- groovy - yourpackage -- MyClass.groovy, 
HelperClass.groovy

and make your build.gradle to be like

    apply plugin : 'groovy'
    apply plugin : 'application'
    mainClassName='MyClass'

    dependencies {
       compile 'org.codehaus.groovy:groovy-all:2.0.0'
       compile '..... instead of @Grab, put all other maven coordinates
    here as compile lines ...'
    }

Running distZip task in Gradle will give you a zip which you can expand 
elsewhere and just run the script which is in the bin folder.



On 08/03/2016 11:05, Raphael Bauduin wrote:
> I have a groovy class with a main that has to be run, another help 
> class in Groovy, and a bunch of jars needed by the app in 
>  ~/.groovy/lib/.
>
> I got it working by using these lines (replacing what I had in the 
> initial config):
>
>     from configurations.runtime.asFileTree.files.collect { 
> zipTree(it).matching{exclude{it.path.contains('DSA') or 
> it.path.contains('RSA') or it.path.contains('SF') }} }
>     from configurations.compile.collect {
>               it.isDirectory() ? it : 
> zipTree(it).matching{exclude{it.path.contains('DSA') or 
> it.path.contains('RSA') or it.path.contains('SF') }}
>     }
>
>
> This removes the signatures of the included jars. I am not familiar 
> with this so I'm not sure about the implications.
> I'll read your suggestions with interest!
>
> Thanks
>
>
>
> On Tue, Mar 8, 2016 at 11:45 AM, Schalk Cronjé <ysb33r@gmail.com 
> <mailto:ysb33r@gmail.com>> wrote:
>
>     I can spot a number of issues in your Gradle script, howver I need
>     to understand context.
>
>     [1] Are you trying to put a single Groovy script + required Groovy
>     JARs into a JAR?
>
>     OR
>
>     [2] Are you trying to build a proper Groovy application consisting
>     of a coouple of class files en dependent JARs?
>
>
>     On 08/03/2016 10:33, Raphael Bauduin wrote:
>
>
>         Hi,
>
>         I'm trying to package a groovy script as a jar with the help
>         of gradle,
>         I use this gradle config: http://pastebin.com/RFEhzMCp
>
>         it builds fine, but when I try to run it with java -jar
>         path_to.jar
>         I get this error:
>         Error: A JNI error has occurred, please check your
>         installation and try again
>         Exception in thread "main" java.lang.SecurityException:
>         Invalid signature file digest for Manifest main attributes
>
>         The only suggestions I found online applied when people
>         repackaged jars, which is not my case.
>         Any suggestion?
>
>         Thanks
>
>         Rb
>
>
>
>     -- 
>     Schalk W. Cronjé
>     Twitter / Ello / Toeter : @ysb33r
>
>
>
>
> -- 
> Web database: http://www.myowndb.com
> Free Software Developers Meeting: http://www.fosdem.org


-- 
Schalk W. Cronjé
Twitter / Ello / Toeter : @ysb33r