You could rename the file from "GenomeAnalysisTKLite.jar" to "GenomeAnalysisTK.jar" in the directory where you placed GATK...

Something like

/home/svcgalaxy/g/tool-data/shared/jars/gatk

and it should work...

Thon

On Jan 03, 2013, at 02:54 PM, mark.rose@syngenta.com wrote:

Hello   Is it possible to redirect the GATK tools in my local installation of Galaxy to use GATK Lite (which is free) rather than GATK.  If so what files would need to be altered and how?  I’m particularly interested in getting the “Depth of Coverage” tool to work.   Thanks much   Mark

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