Thanks again Nate.
You are right that SGE is overwriting TMPDIR.
When the job runs, TMPDIR is actually set to a job specific dir like
/tmp/3579.1.default.q
It seems that I will have to change the SGE queue settings so that TMPDIR
only set the "prefix" to /scratch that I want... but this would aff
On Aug 18, 2013, at 1:58 AM, tin h wrote:
> Thanks Nate!
>
> I did think that job_conf.xml would overwrite settings in universe_wsgi.ini.
> I rewrote it and see that the galaxy job gets to run on the cluster.
> However, the TMPDIR clause defined in nativeSpecification didn't seems to be
> e
Thanks Nate!
I did think that job_conf.xml would overwrite settings in
universe_wsgi.ini. I rewrote it and see that the galaxy job gets to run on
the cluster. However, the TMPDIR clause defined in nativeSpecification
didn't seems to be effective :(
the console output "log" does not show what t
On Aug 14, 2013, at 9:46 PM, tin h wrote:
>
> Hello gurus,
>
>
> I made some slight progress...
>
> If I specify a handlers section into the job_conf.xml file with:
>
>
>
>
>
> Then galaxy would at least start. However, it is not very functional, I
> can't upload files
Hello gurus,
I made some slight progress...
If I specify a handlers section into the job_conf.xml file with:
Then galaxy would at least start. However, it is not very functional, I
can't upload files or run job, it says:
An error occurred with this dataset:*Unable to run j
Original Message
Subject: Re: how to add settings of TMPDIR=/scratch for sge/drmaa in
universe_wsgi.ini
Date: Tue, 13 Aug 2013 23:21:16 -0700
From: tin h
To: Jennifer Jackson
CC: Galaxy Dev
Thank you Jennifer.
I am not sure if my previous email got gabled u
Thank you Jennifer.
I am not sure if my previous email got gabled up...
Just to be sure, I specified the following in universe_wsgi.ini
default_cluster_job_runner = drmaa://-q default.q -V -v
TMPDIR=/scratch/
when i start galaxy, looking at the console log, this is what I see:
galaxy.jobs
Hi Tin,
I am going to move this over to the galaxy-...@bx.psu.edu mailing list
(good for local install questions) to give it better viability.
I am by no means the best person to help with this, so hopefully others
will jump in, but just from looking at this I am wondering if you
shouldn't b
