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> > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
