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_the_Galaxy_Web_API
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%20Scaling
Hope this helps,
Dave C.
On Mon, Sep 19, 2011 at 9:51 AM, Oren Livne <li...@uchicago.edu
<mailto:li...@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
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at 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
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