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
That was easy to resolve since the jar file is located at either
/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?
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
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