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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