https://bitbucket.org/ichorny/galaxy-central-ilya2/pull-request/new

everything but the tophat/cufflinks wrapper.

Thanks,

Ilya


-----Original Message-----
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu] 
Sent: Friday, October 21, 2011 12:56 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Re Acutal user code

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/__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.

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 code?

Thanks,
--nate

> 
> Thanks,
> 
> Ilya
> 
> 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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