Ann Black wrote:
> 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.
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 to
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 environm
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 gal
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
te: 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 wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I
can see jobs getting submitted
> 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 q
arch
> >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
> &g
ormatics Support
Ontario 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
>
, 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 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 pat
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 user
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
13 matches
Mail list logo
