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   This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/