Hej
Thanks for your input.
--
Jonas Hagberg
BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se
e-mail: jonas.hagb...@bils.se, jonas.hagb...@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 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
> 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.hagb...@bils.se, jonas.hagb...@scilifelab.se
> > phone: +46-(0)70 6683869
> > address: SciLifeLab, Box 1031, 171 21 Solna, Sweden
> >
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