On Tue, Jul 30, 2013 at 5:27 PM, Ketan Maheshwari <ketancmaheshwari@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