It seems like GATK authors at Broad really really want you to phone home every time you use their software. I'm getting this error while running the lastest version: "ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for more information and instructions on how to obtain a key."

From the Phone_home wiki page:

"How to Obtain a GATK Key To obtain a GATK key, email gsahelp@broadinstitute.org with the subject line GATK Key Request. In your email, please provide us with the reason(s) you need to run the GATK with the phone-home feature disabled. Please be as explicit as possible about why you cannot participate in the phone home feature. Note that the key you will be issued is linked to the email address you used to contact us."

In general I don't have an issue with phone home features from software providers I trust, and I do completely trust The Broad Institute. Although, this does sound a little draconian how is being imposed.

Nevertheless, I would like to ask for an easier way to deactivate the use of "-et NO_ET" on Galaxy GATK's wrappers. Right now I'm manually commenting the relevant line, but I think this means my mercurial repository won't get any update from upstream, or that I will have to deal with merging.

Regards, Carlos