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