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 <greg@bx.psu.edu>
> > To:
Liisa Koski <liisa.koski@dnalandmarks.ca>
> > Cc:
jen@bx.psu.edu, galaxy-user@lists.bx.psu.edu, galaxy-user-bounces@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 <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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> > >
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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
> > greg@bx.psu.edu
> >
> >
> >
>
> Greg Von Kuster
> Galaxy Development Team
> greg@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/