You can also only pull the 5589 changeset - this one *just* missed the
stable release (stable is at 5588):

  % hg pull -r 316f79f7bc1a https://bitbucket.org/galaxy/galaxy-central/
  % hg update

--nate

Greg Von Kuster wrote:
> 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
> 
> 
> 

> ___________________________________________________________
> 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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