...@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 code
It seems to be working but when I run BWA or Bowtie it finishes green but the
files are empty. Doesn't give
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
close to being ready to integrate. The major outstanding issue is to try to
avoid
[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
: [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
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,
: 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
@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
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 having a
