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.witham@jax.org
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