Hi James,

Since genomic data files are often very large, Galaxy does not store them in a database, so this specific scenario has not been implemented as far as I know.  However, you may be able to implement what you've described without too much difficulty.  If you could implement a layer on top of your database that leverages Galaxy's features for uploading a directory of files or file system paths (maybe better in this case) without copying the data into Galaxy's default file store, it should be fairly trivial to make Galaxy work with it.  Using this combination, Galaxy will read the data (without making any changes to it) in order to generate metadata associated with the data.  The metadata is stored separately from the raw data.

I was at the Pac Bio meeting, so we definitely met there.  Good to hear from you!

On Nov 7, 2011, at 8:58 PM, James Ireland wrote:

Hi Greg,

Thanks for the fast response!  I think we might have met last year at the PacBio 3rd party software vendor meeting.

So, I had seen the documents for the data repository and the"Uploading a Directory of Files" with the "Copy data into Galaxy?" option de-selected seems the closest analog to what I want to do.  In my complete and utterly naive understanding of how Galaxy works, if I could wrap my data repository (in this case, my db) with the same sort of functionality as a file directory (scan, load, etc) then I would guess that the integration wouldn't be that painful.  Obviously, this would require custom development.  This is important enough to my company that we'd be willing to work on doing this - but I'm guessing I'm way off base?

This seems like it would be a fairly common request - to your knowledge, has anyone outside Galaxy rolled their own solution along these lines?

Thanks again,
-J
 

On Mon, Nov 7, 2011 at 11:41 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello James,

This is not currently possible - the options for uploading files to Galaxy data libraries is documented in our wiki at http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

On Nov 7, 2011, at 2:11 PM, James Ireland wrote:

Greetings!

I would like to expose data I have in a relational database as a data library in Galaxy.  I would really like to do this without Galaxy having to make a local copy of the data to the file system.  Is this possible and could you point me to any code examples and/or documentation?

I'm sure this must be covered somewhere in the documentation or mailing list, but I haven't been able to find it. 

Thanks for your help!

-James
--
J Ireland
www.5amsolutions.com | Software for Life(TM)
m: 415 484-DATA (3282)
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J Ireland
www.5amsolutions.com | Software for Life(TM)
m: 415 484-DATA (3282)

Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu