' is not defined
Removing PID file main.pid
--
Branden Timm
bt...@energy.wisc.edu
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should be submitted.
--
Branden Timm
bt...@energy.wisc.edu
On 6/5/2013 10:58 AM, Branden Timm wrote:
Hi All,
Just did an update to HEAD, and upon restarting the daemons received
the following messages:
galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083
in condor runner
of the output file from my job
leads me to believe it finished just fine, and indicating failure to the
user because Galaxy couldn't cleanup a 1b error code file seems a little
extreme to me.
Thanks!
--
Branden Timm
bt...@energy.wisc.edu
of the output file from my job
leads me to believe it finished just fine, and indicating failure to the
user because Galaxy couldn't cleanup a 1b error code file seems a little
extreme to me.
Thanks!
--
Branden Timm
bt...@energy.wisc.edu
, Branden Timm wrote:
I recently upgraded to the latest galaxy-central, and was advised on
first run that two tools in tool_conf.xml had been removed from the
distribution, but could be installed from the tool shed. I ran the
script that it generated, however the script fails with the following
messages
'BlastXml'
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Branden Timm
bt...@energy.wisc.edu
On 5/8/2013 10:17 AM, Nate Coraor wrote:
On May 8, 2013, at 10:08 AM, Branden Timm wrote:
Hi All,
I've been working to configure a new Galaxy instance to run jobs under
Condor. Things are 99% working at this point, but what seems
. Thanks!
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Branden Timm
bt...@energy.wisc.edu
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or to just install 2.6 alongside 2.7.
--
Branden Timm
bt...@glbrc.wisc.edu
On 2/2/2011 12:07 PM, Peter Cock wrote:
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborneozb...@uab.edu wrote:
I have (or rather had) a functional galaxy installation on a CentOS box
running python 2.4. I did an mecurial update
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes Bioenergy Research Center
bt...@wisc.edu
On 4/19/2011 10:45 AM, Branden Timm wrote:
Hi All,
I'm having issues running BWA for Illumina with the latest version
of Galaxy (5433
it seems that even using data tables, the format of my .loc
files shouldn't need to change because they both use four columns
separated by tabs.
As always, any help is greatly appreciated.
--
Branden Timm
bt...@glbrc.wisc.edu
On 4/26/2011 12:29 PM, Vipin TS wrote:
Hi Branden,
I find
to map against is correct (all
whitespace is tab characters):
synpcc7002 synpcc7002 Synechococcus
/home/galaxy/galaxy-central/bwa_
indices/SYNPCC7002
I'm not sure what the next troubleshooting step is, any ideas?
--
Branden Timm
bt...@glbrc.wisc.edu
section. However, the second occurrence of the tool is not displayed.
Is it possible to list the same tool twice under the same section?
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Branden Timm
bt...@glbrc.wisc.edu
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(thanks for
letting us know it was out of date!).
Regards,
Kelly
On Jan 13, 2011, at 11:39 AM, Branden Timm wrote:
Thanks for the tip, Kelly - I tested this on my workstation at
revision 4640 and am seeing the same behavior. The output SAM file
is 1.9G. I will pull the latest changes from
it on the command line. The tool completes
successfully in a few minutes, which confirms that the Galaxy server
process seems to be the culprit in this situation, not bowtie_wrapper.
Any help would be greatly appreciated. Cheers
--
Branden Timm
University of Wisconsin
Great Lakes Bioenergy Research
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