Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, 
and when I try to run Count Covariates I get the error: ERROR stack trace 
org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with 
name 'T' isn't defined. at org.broadinstitute.s

I have looked at the GATK Count Covariates command line, and it looks to me 
like the argument with name 'T' is not a place where I need to input a file, 
but is where the Count Covariates software information goes. I get this same 
error when trying to run Realigner Target Creator.

I wondered if this might be something that could be simply fixed by 
reinstalling the wrappers for GATK, or something along those lines?
  Thank you!


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