@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Re Acutal user code
I am pulling and testing as we speak. I did a preliminary test on my VM but it
does not have enough memory to run BWA. We pull into my dev version on the
cluster and do further testing. Also need to test how it integrates with the
t; To: Chorny, Ilya
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Re Acutal user code
>
> Hi Ilya,
>
> I made a few more commits this morning. Could you test it out in the present
> state? If everything works properly in your environment, I think it's pretty
>
-Original Message-
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
Sent: Wednesday, November 02, 2011 9:15 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Re Acutal user code
Hi Ilya,
I made a few more commits this morning. Could you test it out in the
shutil.rmtree( self.working_directory )
> > in jobs.cleanup(), it'll leave everything behind.
> >
> > --nate
> >
> > >
> > > Thanks,
> > >
> > > Ilya
> > >
> > >
> > > -Original Message-
> > > From: ga
nal Message-
> > From: galaxy-dev-boun...@lists.bx.psu.edu
> > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
> > Sent: Monday, October 31, 2011 8:37 PM
> > To: Nate Coraor (n...@bx.psu.edu)
> > Cc: galaxy-dev@lists.bx.psu.edu
> > Subj
Message-
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
> Sent: Monday, October 31, 2011 8:37 PM
> To: Nate Coraor (n...@bx.psu.edu)
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Re Acutal user
: [galaxy-dev] Re Acutal user code
It seems to be working but when I run BWA or Bowtie it finishes green but the
files are empty. Doesn't give me much information. I also tried fastqc and it
ran just fine.
-Original Message-
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
>
> > 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
-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
> > Su
y-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/_
ists.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 s
: [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
@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
: 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
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.b
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 directio
Hey Ilya,
I'm looking at it now, I'll let you know asap (should be tomorrow).
--nate
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 havi
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 kno
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