On Tue, Jul 30, 2013 at 5:27 PM, Ketan Maheshwari
<ketancmaheshw...@gmail.com> 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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

Reply via email to