Hi,
We are getting ready to run a local setup of Galaxy here at bristol university
on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and
now we want to install it properly on the main cluster and have the galaxy
instance run in the queue along with all the other HOC
HI Jeremy,
Many thanks for the feedback (I thought I'd cc'd the dev list but apparently
not!) any advice is most useful especially as they are keen to hear what we
want (they already have a list of demands from the aerospace guys!).
Best Wishes,
David.
__
Dr
Hi,
We seem to have sorted out the problem of TopHat failing to run but now we have
a new problem. When TopHat runs with a large genome (but not with small
genomes), it finishes the run fine and all the data is there but the web
interface falls over about 8 hours into the run and when we try
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax. +44 117 3312091
d.a.matth...@bristol.ac.uk
On 12 Dec 2011, at 21:28, Nate Coraor wrote:
On Dec 12, 2011, at 5:25 AM, David Matthews wrote
Dec 2011, at 21:28, Nate Coraor wrote:
On Dec 12, 2011, at 5:25 AM, David Matthews wrote:
Hi,
Many thanks for the feedback. Sorry about missing some of the traceback,
here is the full traceback:
Exception happened during processing of request from ('xxx.xxx.xxx.xxx',
32781)
Traceback
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax. +44 117 3312091
d.a.matth...@bristol.ac.uk
On 19 Dec 2011, at 15:56, Nate Coraor wrote:
On Dec 14, 2011, at 6:13 PM, David
Hi,
We emailed previously about possible memory leaks in our installation of Galaxy
here on the HPC at Bristol. We can run Galaxy just fine on our login node but
when we integrate into the cluster using pbs job runner the whole thing falls
over - almost certainly due to a memory leak. In
back to you,
so you that you know that this doesn't need to be posted again.
Thanks!
Jen
Galaxy team
On 3/14/12 6:48 AM, David Matthews wrote:
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect
Hi Jen,
Many thanks for this, much appreciated. Will give it a try - fingers crossed!
David.
Sent from my phone, so please excuse my mistakes.
-Original Message-
From: Jennifer Jackson
Sent: 20/03/2012 18:32
To: David Matthews; Galaxy Dev
Cc: galaxy-user; Jeremy Goecks
Subject: Re
