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
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
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
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
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
, 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
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
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
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
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
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