I found the statement in  __init__.py but not in upload_common.py.

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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