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,
Thanks! Working now :) Liisa From: Nate Coraor <nate@bx.psu.edu> To: Greg Von Kuster <greg@bx.psu.edu> Cc: Liisa Koski <liisa.koski@dnalandmarks.ca>, galaxy-user@lists.bx.psu.edu Date: 2011-05-31 14:02 Subject: Re: [galaxy-user] biomart error 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: 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/ = ====================================================================
___________________________________________________________ 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:
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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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ 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:
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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:
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