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.

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&gt; 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 > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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&gt; wrote: > On Jul 22, 2014, at 2:13 PM, John Chilton <jmchilton(a)gmail.com&gt; 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&gt; 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 > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > >