So it looks like for some reason galaxy is not picking up the information in 
the .e file. Not sure why. I even switched it back to writing the files to the 
pbs directory and it still did not pick up the .e files. BWA was core dumping 
but I was not given the error message in galaxy. 

BTW, I find it nice to be able to see the .o and .e files. The way you have it 
coded the .o and .e are written out to the job_working_directory and then 
disappear at the end of the run.  But the way I had it coded the pbs directory 
is world read writable. Is there an issue with having the pbs directory be 
world read write?

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: 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 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]
Sent: Monday, October 31, 2011 1:21 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Re Acutal user code

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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> > 
> > ___________________________________________________________
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> > lists, please use the interface at:
> > 
> >   http://lists.bx.psu.edu/
> > 
> 

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