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 (nate@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, October 21, 2011 2:07 PM To: Nate Coraor (nate@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 (nate@bx.psu.edu) [mailto:nate@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: ichorny@illumina.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com
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