Re: [galaxy-dev] cluster path question

2011-09-12 Thread Ann Black
Hello everyone - I am also running into this issue trying to get galaxy integrated with our sun grid engine. My galaxy user's .bash_profile does not appear to get sourced when the jobs run. I augmented the sample sam_filter.py tutorial such that it output path and user info so I could see how

Re: [galaxy-dev] cluster path question

2011-09-12 Thread Ann Black
I figured out a solution. The sun grid engine will strip back the env of what gets passed along with the job submission. I added a native drmaa option, -V, which caused the env vars found on the shell that submits the job to be passed along. Therefore all the environment setup I did in my

Re: [galaxy-dev] cluster path question

2011-09-12 Thread Nate Coraor
Ann Black wrote: I figured out a solution. The sun grid engine will strip back the env of what gets passed along with the job submission. I added a native drmaa option, -V, which caused the env vars found on the shell that submits the job to be passed along. Therefore all the environment

Re: [galaxy-dev] cluster path question

2011-09-12 Thread Ann Black
Thanks Nate! I did not know about sge_request - and that helps. I played around with using -V and -v in sge_request some and it works similar to specifying -V (or -v) in my universe_wsgi.ini file. I am new to galaxy and I am working on getting it instantiated locally. Is there an advantage

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Ryan Golhar
Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Zhibin Lu
, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Ryan Golhar
Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Nate Coraor
From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Glen Beane
Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Ryan Golhar
From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing