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.
~Aaron