Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any
difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
Marina Gourtovaia wrote:
Hello
My Galaxy instance suffers from 'MySQL server has gone away error'.
This error appears if the last web request was more
Hello
I've set up Galaxy to use LSF. My first job has failed because Galaxy
submitted it to the default queue, which was wrong in my case. However,
Galaxy gracefully survived the failure, I was able to get the job number
from the console output and figure out what went wrong.
Next time I
Try adding
export SGE_ROOT=/directory where drmaa sits or one-two higher
I had a similar problem compiling a perl wrapper for drmaa (LSF). I
found this SGE_ROOT used in the makefile for generating a SWIG perl
wrapper for the drmaa.h header. And also there were some assumptions
about the
Hi
In a bash shell, I define the path (needed both by Galaxy to find the
right version of python and by tools that run on a cluster to find the
executables) and some other global variables on the command line. The
cluster jobs (LSF) inherit all these values. This is my line
On 21/02/2011 16:20, Nate Coraor wrote:
Marina Gourtovaia wrote:
Hi
In a bash shell, I define the path (needed both by Galaxy to find
the right version of python and by tools that run on a cluster to
find the executables) and some other global variables on the
command line. The cluster jobs
Hi
Our production pipeline does this on LSF through job arrays. It would be
good if Galaxy supported job arrays
Marina
On 15/04/2011 13:14, Leandro Hermida wrote:
Hi everyone,
I was wondering what would be the way in Galaxy to program the following:
- User clicks on a tool and form is
Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution
downloaded yesterday
tool file=indels/indel_table.xml /
should be
tool file=indels/indel_table.xml /
?
Marina
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England
Hi Leandro
From our previous correspondence I remember that you are using LSF
This is some sort of a bug in the latest drmaa-lsf binding. I moved to
the previous version and everything is OK for me
Marina
On 18/05/2011 16:15, Leandro Hermida wrote:
Hi all,
I enabled DRMAA on my test Galaxy
Yes. M.
On 18/05/2011 18:23, Leandro Hermida wrote:
Hi Marina,
Thanks... so are you using 1.0.3 instead of 1.0.4?
best,
leandro
On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia m...@sanger.ac.uk
mailto:m...@sanger.ac.uk wrote:
Hi Leandro
From our previous correspondence I
Hi Leandro
I do not think the binding is env var aware. I used the following string
in Galaxy drmaa configuration in universe_wsgi.ini
default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
-q for the queue and -P for the project
Marina
On 19/05/2011 12:54, Leandro Hermida wrote:
Hi
default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
works for me on LSF, so your syntax seems to be correct.
Assuming that -l mem=4gb:nodes=1:ppn=6 works teh way you expect when you
start the jobs on your cluster from the shell, read on...
Bearing in mind the the value of the
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