Dear Galaxy mailing-list,

Once again I come seeking for your help. I hope someone already had this 
issue or will have an idea on where to look to solve it. :)

One of our users reported having workflows failing because some steps were 
executed before all their inputs where ready.
You can find a screenshot attached, where we can see that step (42) "Sort 
on data 39" has been executed while step (39) is still waiting to run 
(gray box).

This behaviour has been reproduced with at least two different Galaxy 
tools (one custom, and the sort tool which comes standard with Galaxy).
This behaviour seems to be a little bit random, as running two times a 
workflow where this issue occurs, only one time did some steps were 
executed in the wrong order.

I could be wrong, but I don't think this issue is grid-related as, from my 
understanding, Galaxy is not using SGE job dependencies functionality.
I believe all jobs stays in some internal queues (within Galaxy) until all 
input files are ready, and only then the job is submitted to the cluster.

Any help or any hint on what to look at to solve this issue would be 
greatly appreciated.
We have updated our Galaxy instance to August 12th distribution on October 
1st, and I believe we never experienced this issue before the update.

Many thanks for your help,
Jean-Fran├žois


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