Re: ASMS Follow Up

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Re: ASMS Follow Up

Bart Gottschalk
What version of Galaxy did you clone and are running when you get this error?  


Once we have this answer we can help you debug the error.  


On Mon, Oct 21, 2013 at 8:25 AM, John Chilton <[hidden email]> wrote:


---------- Forwarded message ----------
From: Gerben Menschaert <[hidden email]>
Date: Mon, Oct 21, 2013 at 4:40 AM
Subject: Re: ASMS Follow Up
To: John Chilton <[hidden email]>


Hello John Mitchel,

I hope you can help out.
PeptideShaker used to be on our Galaxy-P environment, but I removed it.
I'm trying to re-install it again from the toolshed.

While doing so, I bumped into the following error (see below).

Could you point me in the good directory.


Many thanks in advance,
Gerben Menschaert


PS: Also, is there a special GALAXY-P user/development mailing list?


 KeyError: 'tool_panel_section'
URL: http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%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&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__          view
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request          view
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:221 in decorator          view
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:850 in prepare_for_install          view
>>  repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=False )
Module tool_shed.galaxy_install.repository_util:338 in handle_tool_shed_repositories          view
>>  new_tool_panel_section=new_tool_panel_section )
Module tool_shed.util.repository_dependency_util:149 in create_repository_dependency_objects          view
>>  common_install_util.activate_repository( trans, installed_tool_shed_repository )
Module tool_shed.util.common_install_util:36 in activate_repository          view
>>  tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'





On Jun 17, 2013, at 4:52 PM, John Chilton <[hidden email]> wrote:

On behalf of myself and my colleague Jim Johnson, I wanted to thank
you for dropping by one or both of our posters. You can find digital
copies of both poster below.

"Reproducible Proteomic Workows using Extensions to the Galaxy Framework"
http://getgalaxyp.org/documents/asms2013_galaxy_extensions.pdf

"Building Proteomic Application Platforms for Cloud Computing
Environments with CloudBioLinux"
http://getgalaxyp.org/documents/asms2013_cloud_computing.pdf

We had a great time last Monday and agree that a lot of good ideas
were generated. If you have specific questions, comments, or
suggestions please do not hesitate to drop us a line. (I have cc'ed
Jim Johnson, as well Dr. Pratik Jagtap the Galaxy-P project manager,
Dr. Ben Lynch the head of application development at MSI, and Dr.
Timothy Griffin the principle investigator for Galaxy-P on this
e-mail. Feel free to direct questions to whomever you feel is most
appropriate.)

You can find more information about Galaxy-P at http://getgalaxyp.org/
and try our public server at https://usegalaxyp.org/. You can find
more information about Galaxy more broadly at
http://galaxyproject.org/ and CloudBioLinux at
http://cloudbiolinux.org/. All of our source code is open source and
available at various places on BitBucket and GitHub, if you are
interested in any particular part of what we have done let me know
which and I can point you to it.

Thanks again,
-John

------------------------------------------------
John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: <a href="tel:612-625-0917" value="+16126250917" target="_blank">612-625-0917
Cell: <a href="tel:612-226-9223" value="+16122269223" target="_blank">612-226-9223




_______________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: ASMS Follow Up

Gerben Menschaert
Hi,
We are running the galaxyp-central.
Thanks in advance,
Gerben


On Oct 21, 2013, at 4:19 PM, Bart Gottschalk <[hidden email]> wrote:

What version of Galaxy did you clone and are running when you get this error?  


Once we have this answer we can help you debug the error.  


On Mon, Oct 21, 2013 at 8:25 AM, John Chilton <[hidden email]> wrote:


---------- Forwarded message ----------
From: Gerben Menschaert <[hidden email]>
Date: Mon, Oct 21, 2013 at 4:40 AM
Subject: Re: ASMS Follow Up
To: John Chilton <[hidden email]>


Hello John Mitchel,

I hope you can help out.
PeptideShaker used to be on our Galaxy-P environment, but I removed it.
I'm trying to re-install it again from the toolshed.

While doing so, I bumped into the following error (see below).

Could you point me in the good directory.


Many thanks in advance,
Gerben Menschaert


PS: Also, is there a special GALAXY-P user/development mailing list?


 KeyError: 'tool_panel_section'
URL: http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%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&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__          view
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request          view
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:221 in decorator          view
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:850 in prepare_for_install          view
>>  repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=False )
Module tool_shed.galaxy_install.repository_util:338 in handle_tool_shed_repositories          view
>>  new_tool_panel_section=new_tool_panel_section )
Module tool_shed.util.repository_dependency_util:149 in create_repository_dependency_objects          view
>>  common_install_util.activate_repository( trans, installed_tool_shed_repository )
Module tool_shed.util.common_install_util:36 in activate_repository          view
>>  tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'





On Jun 17, 2013, at 4:52 PM, John Chilton <[hidden email]> wrote:

On behalf of myself and my colleague Jim Johnson, I wanted to thank
you for dropping by one or both of our posters. You can find digital
copies of both poster below.

"Reproducible Proteomic Workows using Extensions to the Galaxy Framework"
http://getgalaxyp.org/documents/asms2013_galaxy_extensions.pdf

"Building Proteomic Application Platforms for Cloud Computing
Environments with CloudBioLinux"
http://getgalaxyp.org/documents/asms2013_cloud_computing.pdf

We had a great time last Monday and agree that a lot of good ideas
were generated. If you have specific questions, comments, or
suggestions please do not hesitate to drop us a line. (I have cc'ed
Jim Johnson, as well Dr. Pratik Jagtap the Galaxy-P project manager,
Dr. Ben Lynch the head of application development at MSI, and Dr.
Timothy Griffin the principle investigator for Galaxy-P on this
e-mail. Feel free to direct questions to whomever you feel is most
appropriate.)

You can find more information about Galaxy-P at http://getgalaxyp.org/
and try our public server at https://usegalaxyp.org/. You can find
more information about Galaxy more broadly at
http://galaxyproject.org/ and CloudBioLinux at
http://cloudbiolinux.org/. All of our source code is open source and
available at various places on BitBucket and GitHub, if you are
interested in any particular part of what we have done let me know
which and I can point you to it.

Thanks again,
-John

------------------------------------------------
John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: <a href="tel:612-625-0917" value="+16126250917" target="_blank">612-625-0917
Cell: <a href="tel:612-226-9223" value="+16122269223" target="_blank">612-226-9223





_______________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/