Dear Dave,
This was very useful. Thank you so much. Specifically, I am trying to integrate Galaxy with Condor, which supports DRMAA. Is there an existing Condor job runner implementation, or any useful code for submitting Galaxy jobs to Condor?
Thanks! Oren
On 9/20/2011 12:21 PM, Dave Clements wrote:
Hi Oren,
This book chapter http://userwww.service.emory.edu/~eafgan/content/Galaxy_eScienceGateway.pdf http://userwww.service.emory.edu/%7Eeafgan/content/Galaxy_eScienceGateway.pdf, includes a high-level overview of Galaxy. (Note: that chapter will be copied to the wiki soon.)
There is some API documentation. ~/scripts/api/README, ~/scripts/api/workflow_ execute.py and ~/scripts/api/example_watch_folder.py in the distribution http://wiki.g2.bx.psu.edu/News%20Briefs/2010_07_16#Initial_implementation_of... http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30#API http://wiki.g2.bx.psu.edu/Events/GCC2011 (/Galaxy Deployment and API/ presentation) http://wiki.g2.bx.psu.edu/Admin/Sample%20Tracking/Next%20Gen http://wiki.g2.bx.psu.edu/Events/GCC2011/Workflows%20and%20API
Sometime in the next week I'll compile all this into a single wiki page.
As far as I know there is no "How to write a runner for Galaxy" document. The closest we have is http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster and http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scali...
Hope this helps,
Dave C.
On Mon, Sep 19, 2011 at 9:51 AM, Oren Livne <livne@uchicago.edu mailto:livne@uchicago.edu> wrote:
Dear All, I am a software developer, new to Galaxy. Is there a detailed document about the Galaxy code architecture, API, what runners are, and how to write a runner? I am especially interested in integrating Galaxy with an external scheduler software (I am aware of Galaxy's scheduling capabilities). I'd like to intercept Galaxy workflows and send their object model to my scheduler. I could not find this information on the Galaxy Wiki. Thank you so much in advance, Oren Livne ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/-- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/