Hi Lisa,

Very sorry for the confusion - you are correct!  The tip of the galaxy-dist 
repo at https://bitbucket.org/galaxy/galaxy-dist is change set 5585, so the fix 
is not available in the dist repo yet, and probably won't be there for another 
few weeks.  

If you don't want to wait, you can pull the fix from our development repo at 
https://bitbucket.org/galaxy/galaxy-central.

Greg Von Kuster


On May 31, 2011, at 11:52 AM, Liisa Koski wrote:

> 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
> > 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/
> 
> -- 
> 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 
> 
> 
> 

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



___________________________________________________________
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at usegalaxy.org.  Please keep all replies on the list by
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