On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote:

> Given that it describes where the rest of the files are, maybe it would work 
> to pass only the CONTENTS.json file.
> Then you can just build your references in a  directory structure on a shared 
> file system and keep absolute paths in the CONTENTS.json file.
> If you don't want to modify the tool to accept only the json file, you could 
> write a simple wrapper to read the json and symlink everything into  place 
> before calling your tool.

I think this is the simplest solution for now.

> This is somewhat akin to the reference area galaxy uses to store reference 
> sequences (and their various indices, formats, annotations etc).
> It might be possible to modify galaxy's reference infrastructure to  present 
> these pre-built reference packages in the same way a user chooses hg19, or E. 
> coli K12.  The parse JSON option looks easier to me

This seems like something I should look into, at least. These don't come with 
Galaxy, do they?

> I'm not aware of other galaxy tools that pass "directories" in this way, but 
> they may exist.

I haven't found anyone who seems to be doing the same thing, at least.

> I don't know if you intended to go off-list, feel free to go back on if you 
> want to.

My mistake; I resent my e-mail back on the list as well, but it's pending 
moderation at the moment.


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