Sweet!! Can't wait to see it.

Thanks,

Ilya

-----Original Message-----
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu] 
Sent: Thursday, October 27, 2011 1:24 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Re Acutal user code

Yup, cleaning up some things that were accidentally lost in merges.  I added 
another bitbucket repo so as not to mess up yours.

Chorny, Ilya wrote:
> 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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