I have been trying to figure out how to make the changes you suggested (i.e. 
write output files to the job_working_directory) and then move them over to 
files but I am having a difficult time navigating the code.  If you could point 
me in the right direction, that would be helpful.  I know the 
lib/galaxy/models/ initializes the output files but I don't think 
that is the right place to make the change. This change probably needs to be 
done in the Job_Wrapper but most of the code is very cryptic to me. Any 
guidance would be greatly appreciated. These changes should not take very long 
to implement once I get a handle on the code.



Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582

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