Interact with running job?
Hej I am new to Galaxy. I am reading the documentation but could not really find an answer . I would like to create a tool that when after executed on a cluster the user should be able to interact with the running job. Get the current output and make a plot and see how far the job has come. Clicking on special status link on the running job in history or something like that. How would one do this in galaxy. Is there any way today to do it with the tools in galaxy. Would be great to get some first guidance where to start. cheers -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg@bils.se, jonas.hagberg@scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden
Hello Jonas, I don't believe this is currently doable in Galaxy and it may be difficult to add. I worry that some job/file/cluster configurations Galaxy could be in might not even be setup in such a way that intermediate files, standard output, etc... would not be available to the Galaxy processes until the job is complete. Nonetheless, if you have a fairly simple cluster configuration you could probably output intermediate files/logging files as part of your job and the Galaxy processes would be able to read them. The UI will show these files as "running", but you may be able to hack up the Galaxy framework to provide additional logic and processing. If you do want to do this, I am not entirely sure to start but lib/galaxy/tools lib/galaxy/jobs, templates/webapps/galaxy/history/, static/scripts/mvc/history, static/scripts/mvc/dataset may be places to look. If you come up with some changes to Galaxy that allow supporting this use case or come up with specific recommendations for changes we can make to make Galaxy more amenable, please let us know. A more Galaxy friendly approach might be to break up your job into several jobs/tools and string them together with a workflow. This would allow users to inspect intermediate results as the workflow is processed. I understand though most jobs/tools cannot be broken up in this fashion. Sorry I could not be of more help, -John On Wed, Oct 16, 2013 at 7:40 AM, Jonas Hagberg <jonas.hagberg@scilifelab.se> wrote:
Hej
I am new to Galaxy. I am reading the documentation but could not really find an answer . I would like to create a tool that when after executed on a cluster the user should be able to interact with the running job. Get the current output and make a plot and see how far the job has come. Clicking on special status link on the running job in history or something like that.
How would one do this in galaxy. Is there any way today to do it with the tools in galaxy. Would be great to get some first guidance where to start.
cheers -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg@bils.se, jonas.hagberg@scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden
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Hej Thanks for your input. -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg@bils.se, jonas.hagberg@scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden On Wed, Oct 16, 2013 at 3:18 PM, John Chilton <chilton@msi.umn.edu> wrote:
Hello Jonas,
I don't believe this is currently doable in Galaxy and it may be difficult to add. I worry that some job/file/cluster configurations Galaxy could be in might not even be setup in such a way that intermediate files, standard output, etc... would not be available to the Galaxy processes until the job is complete.
Nonetheless, if you have a fairly simple cluster configuration you could probably output intermediate files/logging files as part of your job and the Galaxy processes would be able to read them. The UI will show these files as "running", but you may be able to hack up the Galaxy framework to provide additional logic and processing. If you do want to do this, I am not entirely sure to start but lib/galaxy/tools lib/galaxy/jobs, templates/webapps/galaxy/history/, static/scripts/mvc/history, static/scripts/mvc/dataset may be places to look.
Great I guessed I needed to do some extra hack into Galaxy Framework.
If you come up with some changes to Galaxy that allow supporting this use case or come up with specific recommendations for changes we can make to make Galaxy more amenable, please let us know.
Yes I will give it a thought.
A more Galaxy friendly approach might be to break up your job into several jobs/tools and string them together with a workflow. This would allow users to inspect intermediate results as the workflow is processed. I understand though most jobs/tools cannot be broken up in this fashion.
Yes it could be a possibility. I need to talk more to the application guy about this. But I think it is possible.
Sorry I could not be of more help,
Just the help I needed to get started. Many thanks!
-John
On Wed, Oct 16, 2013 at 7:40 AM, Jonas Hagberg <jonas.hagberg@scilifelab.se> wrote:
Hej
I am new to Galaxy. I am reading the documentation but could not really find an answer . I would like to create a tool that when after executed on a cluster the user should be able to interact with the running job. Get the current output and make a plot and see how far the job has come. Clicking on special status link on the running job in history or something like that.
How would one do this in galaxy. Is there any way today to do it with the tools in galaxy. Would be great to get some first guidance where to start.
cheers -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg@bils.se, jonas.hagberg@scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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participants (2)
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Jonas Hagberg