Hi Greg,
I thought I was up to date. When I run the following command I get 'no 
changes found'

hg incoming
real URL is https://bitbucket.org/galaxy/galaxy-dist
comparing with http://www.bx.psu.edu/hg/galaxy
searching for changes
no changes found
[galaxy@galaxy_dist]$
 
Thanks,
Liisa



From:
Greg Von Kuster <g...@bx.psu.edu>
To:
Liisa Koski <liisa.ko...@dnalandmarks.ca>
Cc:
j...@bx.psu.edu, galaxy-user@lists.bx.psu.edu, 
galaxy-user-boun...@lists.bx.psu.edu
Date:
2011-05-31 11:29
Subject:
Re: [galaxy-user] biomart error



Hello Lisa,

I noticed your stack trace in another message you sent - pasted below.  If 
this is the problem you are seeing, then upgrading your Galaxy instance to 
the latest version will fix the problem.  This issue was fixed in change 
set 5589.

This is the exact error I am getting... 

Traceback (most recent call last):
 File "galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job
   job_wrapper.prepare()
 File "galaxy_dist/lib/galaxy/jobs/__init__.py", line 361, in prepare
   self.tool.exec_before_job( self.queue.app, inp_data, out_data, 
param_dict )
 File "galaxy_dist/lib/galaxy/tools/__init__.py", line 1881, in 
exec_before_job
   json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( 
param_dict ) #it would probably be better to store the original incoming 
parameters here, instead of the Galaxy modified ones?
 File "galaxy_dist/lib/galaxy/tools/__init__.py", line 1867, in 
_prepare_datasource_json_param_dict
   rval[ key ] = self._prepare_datasource_json_list( val )
NameError: global name 'val' is not defined



Greg Von Kuster


On May 31, 2011, at 11:06 AM, Liisa Koski wrote:

I am also getting the same error with my local biomart and local galaxy 
installations. 

Thanks, 
Liisa 
  


From: 
Jennifer Jackson <j...@bx.psu.edu> 
To: 
Christophe Klopp <christophe.kl...@toulouse.inra.fr> 
Cc: 
galaxy-user@lists.bx.psu.edu 
Date: 
2011-05-31 09:32 
Subject: 
Re: [galaxy-user] biomart error 
Sent by: 
galaxy-user-boun...@lists.bx.psu.edu




Hello Christophe,

I am unable to duplicate - BioMart appears to be functioning as expected 
this morning. Would you have time to run your query again?

If the problem persists, if you could share your history with me 
(Options -> Share or Publish -> email back link) and list out the exact 
steps that you are performing, that would be very helpful.

Best,

Jen
Galaxy team

On 5/30/11 8:33 AM, Christophe Klopp wrote:
> Hi,
>
> I've tried a simple query in biomart : retrieve all gene locations for
> the Danio rerio in Ensembl 62 and I get an error :
> An error occurred running this job: /failure preparing job
> /
> The same happens with the test site?
>
> Cheers
>
> Christophe/
> /
>
> --
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email:christophe.kl...@toulouse.inra.fr  =
> =http://www.sigenae.org/                                           =
> =http://bioinfo.genotoul.fr/                                       =
> ====================================================================
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
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>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

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