I modified drmaa.py to pass the galaxy users path variable to the actual user. 
As long as the galaxy user's environment is correct then the actual user's 
environment should be correct.  

-----Original Message-----
From: Glen Beane [mailto:glen.be...@jax.org] 
Sent: Monday, October 31, 2011 4:20 PM
To: Chorny, Ilya
Cc: Lloyd Brown; Galaxy Dev List
Subject: Re: [galaxy-dev] Clusters, Runners, and user credentials

Many of us are using the PBS job runner (for TORQUE) and would definitely be 
interested in a port. 

How do you deal with making sure the user's environment is configured properly? 
We use a python virtualenv and load specific module files with tested tool 
versions in our galaxy users startup scripts on our cluster. 

Sent from my iPhone

On Oct 31, 2011, at 6:29 PM, "Chorny, Ilya" <icho...@illumina.com> wrote:

> BTW, I am not sure if PBS works with drmaa. If not then the code will need to 
> be ported to work with pbs.
> 
> 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 3:27 PM
> To: Lloyd Brown; Galaxy Dev List
> Subject: Re: [galaxy-dev] Clusters, Runners, and user credentials
> 
> Lyod,
> 
> See Nate's email below Title: Actual user code. We have been working on 
> implementing this feature in galaxy. The code is still in development but 
> feel free to test it out and let us know how it works for you.
> 
> Best,
> 
> Ilya
> 
> -----Original Message-----
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lloyd Brown
> Sent: Monday, October 31, 2011 2:35 PM
> To: Galaxy Dev List
> Subject: [galaxy-dev] Clusters, Runners, and user credentials
> 
> I'm a systems administrator for an HPC cluster, and have been asked by a 
> faculty member here to try to get galaxy to work on our cluster.
> Unfortunately, there are one or two outstanding questions that I can't seem 
> to find the answer to, and I'm hoping someone here can help me out.
> 
> In particular, is galaxy, and the PBS runner specifically, capable of 
> submitting jobs under specific user names?  Essentially, if I set up galaxy 
> to push jobs to our cluster, will they all show up under one user credential 
> (eg. the "galaxy" user), or can we set it up so that the user logged into 
> galaxy, is used to submit the job?
> 
> This one is kindof a show-stopper, since our internal policies require that 
> all jobs have a specific user credential, with one person per username.
> 
> Thanks,
> Lloyd
> 
> 
> --
> Lloyd Brown
> Systems Administrator
> Fulton Supercomputing Lab
> Brigham Young University
> http://marylou.byu.edu
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