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