Hi Nate,

Any updates?

Thanks,

Ilya


-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 2:24 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Re Acutal user code

One more thing there are some changes in lib/galaxy/tools/__init__.py and 
lib/galaxy/model/__init__.py that are not related to actual user. They look 
like they are toolshed related and may have been changed because to version of 
the file that I copied over was older then galaxy-central. Probably should have 
done a merge first. I can redo it if you like. Let me know.

Ilya


-----Original Message-----
From: Chorny, Ilya
Sent: Friday, October 21, 2011 2:11 PM
To: Chorny, Ilya; Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: Re Acutal user code

Sorry, the link was wrong.

https://bitbucket.org/ichorny/galaxy-central-ilya2/

-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 2:07 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Re Acutal user code

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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