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