I'm building a pipeline which, initially, will use some existing tools and
then I plan on adding some of my own.  In running this though I've run into
a few questions that might have to do with how Galaxy in general works
rather than being tool-specific.

I've made it up to running Realigner Target Creator (part of GATK tools)
and I don't see a convention of specifying what version of GATK it expects
to be installed.  Then, running the tool failed with "Running with the -et
NO_ET or -et STDOUT option requires a GATK Key file." It seems the -et
option is hard-coded into the component without passing a key, which has to
be applied for. I didn't want this at all, so I modified the following file:

galaxy-dist/tools/gatk/realigner_target_creator.xml

and removed the following line:

-et "NO_ET" ##ET no phone home

Then I added the component and tried to run again, still getting the same
error. If I removed that line how is it still part of the call? Is Galaxy
caching the xml tool files? Also, is there a way to see the precise
commands being executed by Galaxy for any particular tool?

Thanks -

Joshua
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