everything but the tophat/cufflinks wrapper.
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
Sent: Friday, October 21, 2011 12:56 PM
To: Chorny, Ilya
Subject: Re: Re Acutal user code
Chorny, Ilya wrote:
> 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/__init__.py 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.
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 code?
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com<mailto:icho...@illumina.com>
> Website: www.illumina.com<http://www.illumina.com>
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