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

Technically, using the drmaa runner with TORQUE is supposed to work.  I
just tried it here to test Ilya's code, and Galaxy was segfaulting when
trying to interact with TORQUE's libdrmaa on setting up the job
template.  I didn't look into it any further, I'm using a fairly old
TORQUE client here, so I suspect it may just be due to that.

--nate

> 
> 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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