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

 
Thanks,
Liisa

From:	Liisa Koski <liisa.koski@dnalandmarks.ca>
To:	jen@bx.psu.edu
Cc:	galaxy-user@lists.bx.psu.edu, galaxy-user-bounces@lists.bx.psu.edu
Date:	2011-05-31 11:11
Subject:	Re: [galaxy-user] biomart error
Sent by:	galaxy-user-bounces@lists.bx.psu.edu

---

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

Thanks,
Liisa
 

From:	Jennifer Jackson <jen@bx.psu.edu>
To:	Christophe Klopp <Christophe.Klopp@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-bounces@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.klopp@toulouse.inra.fr  =
> =http://www.sigenae.org/                                           =
> =http://bioinfo.genotoul.fr/                                       =
> ====================================================================
>
>
>
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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
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please use the interface at:

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___________________________________________________________
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/