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.

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
> 

> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other 
> Galaxy lists, please use the interface at:
> 
>   http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to