On Tue, Jul 30, 2013 at 5:27 PM, Ketan Maheshwari
wrote:
> Hi,
>
> I am a relatively new Galaxy user. I am wondering if there is an example of
> a tool which allows users to view at the stdout/err of a tool live while it
> is still running to get a sense of progress it is making.
>
> The tools I have had experience with so far will save the stdout/err or an
> elaborate report as they are running and those results would be available
> for users only after the tool has completed running.
>
> Admittedly I have not searched through the toolshed exhaustively.
>
> Best,
> --
> Ketan
I'm pretty sure Galaxy won't allow you to view any of stdout/stderr
until the tool has finished - this is especially true if run on a cluster.
However, if the tool's stdout is redirected to an output file shown
in the Galaxy history you should be able to see that as the job
runs.
My MIRA wrapper does this, I have a Python wrapper script
calling MIRA via subprocess and sending MIRA's stdout to
a text file defined as one of the outputs in the Galaxy XML.
http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Note that from Galaxy's point of view it was calling my Python
script which produced a small amount on stdout - which is not
available until the job finishes.
Peter
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