Hi Folks,

I received an email from one of my end users that she was having an issue with 
the "Realigner Target Creator" under NGS:  GATK Tools.  Here's the error:  An 
error occurred running this job: "Unable to access jar file 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar."
  That was easy to resolve since the jar file is located at either 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/GATK/1.4.2/ or 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/GATK/1.6.13/.  I 
modified the xml to point to the /1.4.2 directory and now I get "Could not 
create the Java virtual machine." I have looked at the wrapper for java 
settings and restarted the Galaxy server, but am at a loss. Do you have any 
ideas?

Thanks,

Iry Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org



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