Hello,
I am trying to run GATK on a local galaxy installation. I get the following error:
##### ERROR ---------------------------------------------------------------------------- --------------
##### ERROR A USER ERROR has occurred (version 1.5-21-g979a84a):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Walker requires a reference but none was provided.
##### ERROR ---------------------------------------------------------------------------- --------------
I choose a fasta file from the history.
When I try to run it directly from the server it works fine but not through the galaxy interface. I guess something is incorrect in the wrapper.
Any advice?
Thanks,
Karen