Re: [svtoolkit-help] Cannot invoke ComputeGenomeMask

[Bob H. <han...@br...>]

It should be there in that release.
Perhaps your classpath is wrong?
The main class org.broadinstitute.sv.apps.ComputeGenomeMask is in 
SVToolkit.jar.
-Bob

On 1/25/12 12:24 PM, Periklis Makrythanasis wrote:
>
> Hi,
>
> I have downloaded the svtoolkit_1.03.619.tar.gz package and according 
> to the instructions I found at the wiki, I tried to invoke 
> ComputeGenomeMask in order to create the mask.
>
> I got the following error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> org/broadinstitute/sv/apps/ComputeGenomeMask
>
> Caused by: java.lang.ClassNotFoundException: 
> org.broadinstitute.sv.apps.ComputeGenomeMask
>
>         at java.net.URLClassLoader$1.run(Unknown Source)
>
>         at java.security.AccessController.doPrivileged(Native Method)
>
>         at java.net.URLClassLoader.findClass(Unknown Source)
>
>         at java.lang.ClassLoader.loadClass(Unknown Source)
>
>         at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
>
>         at java.lang.ClassLoader.loadClass(Unknown Source)
>
> Could not find the main class: 
> org.broadinstitute.sv.apps.ComputeGenomeMask.  Program will exit.
>
> I looked at the files included in the tar.gz file and wasn't able to 
> locate the ComputeGenomeMask. Can you please help?
>
> All the best
>
> Periklis
>
> ----------------------------------------------------------
>
> Periklis Makrythanasis, MD, PhD
>
> Department of Genetic Medicine and Development
>
> University of Geneva Medical School,
>
> 1 rue Michel-Servet
>
> 1211 Geneva, Switzerland
>
> tel: +41-22-379-5112 and +41-22-379-5707
>
> fax:+41-22-379-5706
>
> email: Per...@un...
>
> ----------------------------------------------------------
>
>
>
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