Re: [galaxy-user] biomart error
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 BIAINRA 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/
Re: [galaxy-user] biomart error
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 BIAINRA 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/
Re: [galaxy-user] biomart error
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.ko...@dnalandmarks.ca To: j...@bx.psu.edu Cc: galaxy-user@lists.bx.psu.edu, galaxy-user-boun...@lists.bx.psu.edu Date: 2011-05-31 11:11 Subject: Re: [galaxy-user] biomart error Sent by: galaxy-user-boun...@lists.bx.psu.edu 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 BIAINRA 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/ ___ 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/
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 BIAINRA 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 ___ 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
Re: [galaxy-user] biomart error
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 BIAINRA 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
[galaxy-user] biomart error
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 BIAINRA 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/
