Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin. To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible. The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
Michael, Galaxy is all about plugins! Tools, datatypes, batch systems, visualizations, et cetera. Additional ways to extend Galaxy through plugins are very welcome. We just need to make sure that whatever solution is chosen is extremely general. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell <mepcotterell@gmail.com> wrote:
Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin.
To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible.
The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers.
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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James, That's exactly what I was thinking. In my opinion, hooks are the way to go (as seen in my example), but if there's a better way then I'm game for that to. I just want to be able to extend Galaxy without modifying Galaxy itself. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote:
Michael,
Galaxy is all about plugins! Tools, datatypes, batch systems, visualizations, et cetera.
Additional ways to extend Galaxy through plugins are very welcome. We just need to make sure that whatever solution is chosen is extremely general.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell <mepcotterell@gmail.com (mailto:mepcotterell@gmail.com)> wrote:
Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin.
To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible.
The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers.
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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James, Has there been any more talk about this? I'd be willing to work in my reference implementation into central as a pull request, but I don't want to do that unless there is an agreed upon roadmap or something. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, July 16, 2013 at 2:08 PM, Michael E. Cotterell wrote:
James,
That's exactly what I was thinking. In my opinion, hooks are the way to go (as seen in my example), but if there's a better way then I'm game for that to. I just want to be able to extend Galaxy without modifying Galaxy itself.
Thanks!
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote:
Michael,
Galaxy is all about plugins! Tools, datatypes, batch systems, visualizations, et cetera.
Additional ways to extend Galaxy through plugins are very welcome. We just need to make sure that whatever solution is chosen is extremely general.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell <mepcotterell@gmail.com (mailto:mepcotterell@gmail.com)> wrote:
Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin.
To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible.
The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers.
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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participants (2)
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James Taylor -
Michael E. Cotterell