On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote:

> I think I would approach the directory problem with a wrapper script that 
> takes arguments for each of the components needed by the tool.
> The script could lay out the various files as expected in the working 
> directory and call the script. I think that's cleaner than expecting users to 
> build a tar archive with the proper structure.

Sorry if I wasn't more clear: the tools take _the entire directory_ (which we 
call reference packages, to be less ambiguous in the rest of this e-mail) as 
the input, not parts of it passed separately. Building these reference packages 
is not a problem. They're a fundamental part of a lot of analyses we do, and as 
such, we have tools to build them easily. For the Galaxy instance I'm trying to 
set up, though, most of the reference packages that users need will be provided 
as shared data.


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