Hi James,

I haven't gone too far down the implementation path in this area, so I'm 
certainly not aware of the issues you may be discovering.  The key would be to 
implement a layer on top of your database so that Galaxy's data library upload 
component can treat the data contained in your database just like it treats the 
content of a file on the file system.  Since Galaxy must open and read data 
files stored on the file system in order to use them as input to Galaxy tools, 
it should be able to do the same for data made available from a database table 
(I would assume, but again, I'm not completely sure of the potential issues).  
The data files resulting from the execution of these Galaxy tools would of 
course be files on the file system within the Galaxy default file store.

By "external tools" do you mean tools that are not a part of the Galaxy 
instance?  


On Nov 8, 2011, at 5:14 PM, James Ireland wrote:

> Hi Greg,
> 
> Did more digging around today in the Galaxy source and maybe I misjudged the 
> situation.  Although getting a representation of my datasets into Galaxy 
> appears relatively straightforward, at the end of the day reads of raw data 
> and passing data to and from external tools, etc all assumes the data is 
> sitting in a file, correct? 
> 
> Thanks again,
>  -J
> 
> 
> On Mon, Nov 7, 2011 at 6:29 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> 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 <g...@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)
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
>> 
>> 
>> 
>> -- 
>> J Ireland
>> www.5amsolutions.com | Software for Life(TM)
>> m: 415 484-DATA (3282)
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> 
> 
> 
> -- 
> J Ireland
> www.5amsolutions.com | Software for Life(TM)
> m: 415 484-DATA (3282)

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



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