Chorny, Ilya wrote:
> Nate,
> 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.

Hi Ilya,

I'm having a lot of difficulty separating out the actual user code from
the other code in your fork.  Could you create a fork with just this


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