Directly Extracting Results From Galaxy

Question: Directly Extracting Results From Galaxy

9.2 years ago by

We (BioBike) would like to do to Galaxy what Galaxy does to the UCSC browser, that is, be able to UI+programmatically (i.e., without download/upload of tables) get data from Galaxy to BioBike so that a BioBike user can then carry out next-level-up symbolic analysis on the data that has been molded, folded, and joined by Galaxy. Can someone point me to a description of the API that would enable us to do this? Thanks!

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modified 9.2 years ago by Anton Nekrutenko ♦ 1.7k • written 9.2 years ago by Jeff Shrager • 20

9.2 years ago by

Greg Von Kuster • 840

Greg Von Kuster • 840 wrote:

Hello Jeff, Assuming you are starting from Galaxy and you want to send a Galaxy history item ( 1 data file ) from Galaxy to your BioBike application, you should be able to just copy the existing tool config in ~/tools/data_destination/epigraph.xml and make the necessary URL changes to point to your BioBike, adding the new tool to your Galaxy instance. Of course, this also assumes your BioBike app will be able to handle the request from Galaxy. Let me know if you have questions on this. Greg Von Kuster Galaxy Development Team

ADD COMMENT • link written 9.2 years ago by Greg Von Kuster • 840

9.2 years ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k wrote:

Hi Jeff: Let us discuss this a bit and we will get back to you. anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

ADD COMMENT • link written 9.2 years ago by Anton Nekrutenko ♦ 1.7k

Thanks, Anton. I had in mind being able to get the data from a cloud- based Galaxy server, for example, your psu instance, not from one that I run myself. I think that the latter is what Greg described. I take that that you got this, and that's what you are considering. It would be fine, initially, to simply display a temporary REST URL that we could cut/paste into a BioBike field that then tells BioBike how to reach into Galaxy through the back to get the table. Of course, something a little simpler would be better, but in the modern world where everything is Ajax magic, it's pretty hard to make computers talk to one another as smoothly as we would like. Cheers, 'Jeff

ADD REPLY • link written 9.2 years ago by Jeff Shrager • 20

Hello Jeff, I opened the following ticket for this issue - you can "follow" the ticket in bitbucket if you want. http://bitbucket.org/galaxy/galaxy-central/issue/188/directly- extracting-results-from-galaxy Thanks very much for your request. Greg Von Kuster Galaxy Development Team

ADD REPLY • link written 9.2 years ago by Greg Von Kuster • 840

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