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:

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/

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/ = ====================================================================

---

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 greg@bx.psu.edu

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/ = ====================================================================

---

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 greg@bx.psu.edu

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

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:

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/ = ====================================================================

---

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 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/

Hello -

Galaxy main has been updated and I was able to send the D.rerio data from BioMart back to into my test history without any problems. Please give this a try as well and if you continue to have issues, sharing your history with us would be very helpful.

Thank you for your patience and help!

Best,

Jen Galaxy team

On 5/31/11 10:22 AM, Jennifer Jackson wrote:

Hello Christophe,

Very sorry, the Biomart issue was known and addressed in the galaxy-central code repository, but we have determined that is has not yet been applied to the Galaxy main server. We will be doing this shortly.

Once it is done, I will write again. If you would be able to re-test on your end at that time and let us know if things are working as expected, that would be great!

Be in touch soon,

Jen

...

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:

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/