DRMAA broken following SGE update. How to fix?
Hi, Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers, Chris -- Dr Chris Cole Senior Research Associate (Bioinformatics) College of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
BUMP Does anyone have any idea on this? Our Galaxy is currently out of action until this is sorted. Thanks, Chris On 22/08/11 10:08, Chris Cole wrote:
Hi,
Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers,
Chris
Did you adjust the SGE_ROOT environment variable to point to the libdrmaa for SGE (probably /opt/sge_62u5_gr/bin/lx24-amd64) ? This is of course just a guess, could you please provide some error messages/logs ? Cheers, Roman On 2011-08-23 10:20, Chris Cole wrote:
BUMP
Does anyone have any idea on this? Our Galaxy is currently out of action until this is sorted. Thanks,
Chris
On 22/08/11 10:08, Chris Cole wrote:
Hi,
Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers,
Chris
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Hi Chris, Take a look at this file : lib/galaxy/jobs/runners/drmaa.py in your galaxy directory. You can export a path for binaries here. For example : export PATH=$PATH:/opt/bin/ before export PYTHONPATH Moreover, do not forget other path values in your service script or in your galaxy user profile. Hope this help. 2011/8/23 Roman Valls <brainstorm@nopcode.org>
Did you adjust the SGE_ROOT environment variable to point to the libdrmaa for SGE (probably /opt/sge_62u5_gr/bin/lx24-amd64) ?
This is of course just a guess, could you please provide some error messages/logs ?
Cheers, Roman
On 2011-08-23 10:20, Chris Cole wrote:
BUMP
Does anyone have any idea on this? Our Galaxy is currently out of action until this is sorted. Thanks,
Chris
On 22/08/11 10:08, Chris Cole wrote:
Hi,
Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers,
Chris
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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Chris Cole -
remy d1 -
Roman Valls