Are the affected workflow steps actually failing or are they falsely being 
reported as “failed” (have you checked if correct output exists for the 
affected step)? Once a step/job is marked “failed’ you can’t use the output 
(even if it exists) for any subsequent step.

If you are using a cluster for your local galaxy install and NFS disk mounts 
then this may happen because of write cache delays. If that is the case, 
increasing the value for the “retry_job_output_collection” parameter  to a 
higher number in the universe_wsgi.ini should help you get around the problem. 
It fixed the problem in our local galaxy  where some jobs were being reported 
as “failed” though the correct output was there.


From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of J. Greenbaum
Sent: Thursday, May 24, 2012 9:18 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] possible to resume failed workflow?


I've created a few workflows and have been having issues with some steps 
randomly failing.  This would not be an issue if I could simply resume the 
workflow from the failed step, but it seems that this is not possible.  
Instead, I'm forced to restart the workflow from the beginning.  Is this true 
or am I missing something?



Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgb...@liai.org<mailto:jgb...@liai.org>
La Jolla Institute for Allergy and Immunology

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