igrateToolsApplication' object has no attribute 'security'
Any help would be greatly appreciated. Thanks!
--
Branden Timm
bt...@energy.wisc.edu
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in your
eanup cluster files set the
dataset state to ERROR? An inspection 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 seem
eanup cluster files set the
dataset state to ERROR? An inspection 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 seem
1.000, 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
mes
niff_order: 'module' object has no
attribute 'BlastXml'
--
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 unde
Nate, thanks - replacing the data types file worked.
-Branden
On 5/8/2013 11:29 AM, Nate Coraor wrote:
On May 8, 2013, at 12:21 PM, Branden Timm wrote:
Nate, thanks for the tip. I'm adding some debugging info around that block now
to inspect what is going on.
One thing I just remem
uster_files_directory, '%s.condor.log' % galaxy_id_tag )
NameError: global name 'galaxy_id_tag' is not defined
Removing PID file main.pid
--
Branden Timm
bt...@energy.wisc.edu
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hether a patch 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
g and run 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 Bio
page indicates so, but seems a bit outdated. I am
running 0.12.1 currently.
--
Branden Timm
bt...@glbrc.wisc.edu
On 1/13/2011 12:30 AM, Kelly Vincent wrote:
Branden,
Which revision of Galaxy are you using? What this sounds like is that
it is taking a long time to set the metadata on the
7;re using (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 change
section. However, the second occurrence of the tool is not displayed.
Is it possible to list the same tool twice under the same section?
--
Branden Timm
bt...@glbrc.wisc.edu
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file for errors, it seems that the line for
the reference genome I'm trying 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 nex
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
en 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 a wiki documentatio
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 Osborne wrote:
I have (or rather had) a functional galaxy installation on a CentOS box
running python 2.4. I did an mecurial update for the
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