Dear Dave, Victor,
Is it possible to simply use the drmma job runner with the condor drmma
lib.so?
Thanks!
Oren
On 9/22/2011 3:21 PM, Victor Ruotti wrote:
Hi Dave,
That was me!
I'm currently talking with the condor folks here in Madison WI.
It would be great to get galaxy going with Condor since condor nows
forms part of red hat.
Besides the existing available docs that you listed below who do you
think would be best as a contact for questions regarding this
implementation?
best,
Victor
On Sep 21, 2011, at 12:16 PM, Dave Clements wrote:
Hi Oren,
I had no idea so I went to the Galaxy mailing list archive @ Nabble
(http://gmod.827538.n3.nabble.com/Galaxy-f829901.html) and searched
for Condor
(http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=829901&query=condor
<http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=829901&query=condor>).
It appears that Ravi Madduri @ Argonne has done some work with this.
I was also at a meeting in March with someone from Wisconsin (where I
think Condor is currently developed) and they indicated their might
be interest in helping Galaxy work with Condor. I/you can pursue
this option as well.
Dave C.
On Wed, Sep 21, 2011 at 9:38 AM, Oren Livne <[email protected]
<mailto:[email protected]>> wrote:
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 <[email protected]
<mailto:[email protected]>> 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
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the list by
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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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
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:
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