Nate and John,
I managed to make sudo work with galaxy and TORQUE with some fixes:
1. the configuration for external runner/killer/chown cannot be read from
ether universe_wsgi.ini or job_conf.xml.
I haven't looked into why but just hard coded them into the galaxy
source code.
2. drmaa cannot recognize the key word 'arg' and 'email'. Again I did a
dirty fix by deleting them in both drmaa.py
and drmaa_external_runner.py.
3. 'sudo -E' will rename LD_LIBRARY_PATH to LIBRARY_PATH. So I have to
create a wrapper for each of the
three scripts (runner/killer/chown) to correct this.
4. The sudo file should now contain the three wrappers. Here I would like
to point out an error in the user guide.
Even for people who doesn't need the wrappers, the chown script
shouldn't not be '/bin/chown' in the sudo file,
but the python script /path/to/external_chown_script.py.
After these steps, I am able to run galaxy jobs as the real user. Now I
need to see how to fix 1 and 2 in an elegant way.
Ping
On Thu, Jul 24, 2014 at 12:05 PM, Ping Luo <luop0812(a)gmail.com> wrote:
Nate and John,
I tried with pbs-drmaa and it crashed my galaxy server when the server was
started and tried to load the drmaa library .
However, I am able to make the drmaa library that comes with TORQUE
working with galaxy if sudo is not use.. With sudo,
there are still problems I am working to resolve.
Ping
On Thu, Jul 24, 2014 at 10:10 AM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> On Jul 22, 2014, at 2:13 PM, John Chilton <jmchilton(a)gmail.com> wrote:
>
> Running jobs as the "real" user is not available with the PBS job
> runner - one has to use the DRMAA interface to submit jobs as the real
> user.
>
>
> That said, the DRMAA runner plugin is compatible with Torque, you just
> need to compile and use pbs-drmaa, rather than Torque's libdrmaa:
>
>
http://apps.man.poznan.pl/trac/pbs-drmaa
>
> --nate
>
>
> I have created a Trello card to add this functionality:
>
https://trello.com/c/OddS8bMP
>
> Would be happy to field pull requests to add this - because I doubt
> anyone on the core team will be able to get to this anytime soon.
> Sorry I don't have better news.
>
> -John
>
> On Sun, Jul 20, 2014 at 11:26 PM, Ping Luo <luop0812(a)gmail.com> wrote:
>
> I have installed pbs_python module on our cluster to interface Galaxy with
> TORQUE. I am able to submit and run jobs on our cluster as the Galaxy
> user.
> I need to run Galaxy jobs as the real user. The instruction in the user
> guide is for DRMAA interface. How can I configure running jobs as real
> user
> for TORQUE?
>
> thank,
>
> Ping
>
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