Hi James,

Existing tools mostly take file paths. This has arguably useful side
effects in isolating cluster node execution from the galaxy server
process and persisting the computation input on a file-system -
arguably more stable long term than queries on dynamic database tables
- and maybe not somewhere you want or need to invest a lot of effort.

Depends what your users need to make use of existing Galaxy tools - eg
a specific experiment's sequence data in (eg) fastq format? Take a
look under scripts/api - maybe you could write scripted queries into
galaxy libraries automagically. Alternatively, if you want users to
script their own extractions, not hard to write a new Galaxy tool that
writes a new (eg) fastq file based on a database query with parameters
supplied by the user. That fastq file appears in a history where it is
then available for all existing Galaxy fastq tools and is a shareable
persistent object for replicable analysis.

On Tue, Nov 8, 2011 at 9:39 PM, James Ireland <jirel...@5amsolutions.com> wrote:
> Hi Greg,
> So, here are my concerns:
> 1.  From looking through some of the source it *appears* to me that the raw
> data input calls are spread across the various libraries as standard file IO
> calls.  So, if I wanted to use my db underneath I'd need to replace/catch
> all of these.  I was hoping that there would be fewer points of
> customization required.
> 2.  Even solving (1), when tools are called from Galaxy like the SAM tools,
> ClustalW, etc I am assuming that behind the scenes these apps are being
> passed file paths.  I know that's how I've wrapped my own tools in Galaxy.
> So, I would need to instantiate my data to file at that point.  That would
> mean adding some more special sauce to catch whenever a file path is being
> passed out to a tool and make sure the file gets created first.
> My HUGE caveat is that I still haven't spent much time with the source so I
> could be way off on these concerns - but this is my impression.  I'd welcome
> enlightenment if I'm wrong!
> Thanks,
>  -J
> On Tue, Nov 8, 2011 at 3:13 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> 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)
>>>> ___________________________________________________________

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