Chorny, Ilya wrote:
> Sweet!! Can't wait to see it.
Have a look:
https://bitbucket.org/natefoo/galaxy-central-ichorny/
Caveats:
* job_working_directory has to be in a shared filesystem
* outputs_to_working_directory must be True
* set_metadata_externally must be True
One thing that would be good from a security standpoint would be if the
external chown script took a Galaxy Job ID for its argument instead of a
path, and then looked up the working directory path from the ID. That
way the script couldn't be used maliciously to chown any file.
--nate
>
> 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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> >
>
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