I recently ran into a problem where attempting to run a workflow
resulted in an uninformative error and a traceback in the logs, that I
put into Google. This led me to the message below from 2012. As far as
I can see it got no reply at the time and I have hit the same issue.
I modified database/compiled_templates/workflow/run.mako.py and this
resulted in a much more useful error report appearing in the browser.
Obviously this is a generated file, so attached is a patch for
templates/webapps/galaxy/workflow/run.mako that I propose you add to
Galaxy. As you'll see it just adds a single "try" block and then
ignores the exception, which I would say in this case is not actually a
bad thing to do even if it is not the ideal fix. Should be fairly
explanatory from the patch.
Way way back in Jun 2012, Paul-Michael.Agapow at hpa.org.uk wrote:
Looking for pointers on what might be causing this problem:
A user had a moderately complicated workflow that when run under certain parameter values
results in a traceback that ends:
Module workflow_run_mako:232 in render_body
>> for ic in oc.input_step.module.get_data_inputs():
AttributeError: 'WorkflowStep' object has no attribute 'module'
After some puzzling, I realized one of the parameters was outside the allowed range (a
max on an integer param) and that Galaxy was trying to render "run.mako"
flagging up the error but erroring out. Why Galaxy tries to call this non-existent member
is unclear to me. Any insight or places I should start exploring?
Galaxy version: various (started with an 6-month old one, upgraded to latest production
to see if it would fix error, it didn't)
Hosting OS: CentOS 6
Paul Agapow (paul-michael.agapow at hpa.org.uk)
Bioinformatics, Health Protection Agency (UK)
Tim Booth <tbooth(a)ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
+44 1491 69 2705