Chorny, Ilya wrote:
> I found the statement in  __init__.py but not in upload_common.py.

Sorry, it's in a commit newer than the latest stable release.

--nate

> 
> Thanks,
> 
> Ilya
> 
> 
> -----Original Message-----
> From: Nate Coraor [mailto:n...@bx.psu.edu] 
> Sent: Wednesday, June 15, 2011 8:47 AM
> To: Chorny, Ilya
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Passing username to drmaa.py
> 
> Chorny, Ilya wrote:
> > Ok, so I figured out how to get the username in drama.py and pass it along 
> > to SGE(in our case) using the Gordon patch. Now I am getting an error that 
> > "Job output not returned from cluster" which comes from the finish job sub 
> > routine in drama.py . I am assuming this is because the .dat file are owned 
> > by the galaxy user and do not have write permission by other users. Where 
> > are these files created? I am hoping to add a  system call to chmod to see 
> > if this fixes the problem.
> 
> The output files are created in lib/galaxy/tools/actions/*.py.
> 
> __init__.py:
> 
>     # Create an empty file immediately
>     open( data.file_name, "w" ).close()
> 
> upload_common.py:
> 
>     # Create an empty file immediately
>     if not dataset.dataset.external_filename:
>         open( dataset.file_name, "w" ).close()
> 
> --nate
> 
> > 
> > Thanks,
> > 
> > Ilya
> > 
> > 
> > -----Original Message-----
> > From: Nate Coraor [mailto:n...@bx.psu.edu]
> > Sent: Thursday, June 09, 2011 9:47 AM
> > To: Chorny, Ilya
> > Cc: galaxy-dev@lists.bx.psu.edu
> > Subject: Re: [galaxy-dev] Passing username to drmaa.py
> > 
> > Chorny, Ilya wrote:
> > > I am trying to figure out how to pass the current user name to drama.py. 
> > > I have had little success so far. None of the environmental variables 
> > > contain any current user information. Any thoughts?
> > > 
> > > Thanks,
> > > 
> > > Ilya
> > 
> > Hi Ilya,
> > 
> > You can use $__user_email__ in the command template in the tool's 
> > configuration, if you need it there.  In the drmaa.py code itself, you can 
> > use the '.user' property on the job wrapper to get the email address.
> > 
> > --nate
> > 
> > > 
> > > 
> > > Ilya Chorny Ph.D.
> > > Bioinformatics - Intern
> > > icho...@illumina.com<mailto:icho...@illumina.com>
> > > 858-202-4582
> > > 
> > 
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