Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I tested thus far:
--------------------------- Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name' URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:322 in install_repository view
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
Module galaxy.web.controllers.admin_toolshed:804 in build_tool_panel_section_select_field view
options.append( ( tool_section.name, tool_section.id ) )
AttributeError: 'ToolSectionLabel' object has no attribute 'name' ---------------------------
The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to "../toolshedtools" in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy.
Any additional configs to make somewhere? In the original tool_conf.xml file?
Alex
Hi Alex,
The ToolSectionLabel element is causing the problem as it is not currently supported in the new tool shed repository installation implementation. I'll try to get a fix for this today. In the meantime, eliminating the section label from your tool config should work as a temporary workaround. I'll send you a note when I have the fix - sorry for the inconvenience.
FYI - I have a fairly complex change set coming today that will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 3, 2012, at 10:20 AM, Bossers, Alex wrote:
Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I tested thus far:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name' URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:322 in install_repository view
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
Module galaxy.web.controllers.admin_toolshed:804 in build_tool_panel_section_select_field view
options.append( ( tool_section.name, tool_section.id ) )
AttributeError: 'ToolSectionLabel' object has no attribute 'name'
The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to "../toolshedtools" in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy.
Any additional configs to make somewhere? In the original tool_conf.xml file?
Alex
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
This should now be working in change set 6668:84baec18959c, which is available in our central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:05 AM, Greg Von Kuster wrote:
Hi Alex,
The ToolSectionLabel element is causing the problem as it is not currently supported in the new tool shed repository installation implementation. I'll try to get a fix for this today. In the meantime, eliminating the section label from your tool config should work as a temporary workaround. I'll send you a note when I have the fix - sorry for the inconvenience.
FYI - I have a fairly complex change set coming today that will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 3, 2012, at 10:20 AM, Bossers, Alex wrote:
Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I tested thus far:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name' URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:322 in install_repository view
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
Module galaxy.web.controllers.admin_toolshed:804 in build_tool_panel_section_select_field view
options.append( ( tool_section.name, tool_section.id ) )
AttributeError: 'ToolSectionLabel' object has no attribute 'name'
The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to "../toolshedtools" in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy.
Any additional configs to make somewhere? In the original tool_conf.xml file?
Alex
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg, Thanks for quick fixes! I will testdrive them shortly and keep you posted. Currently we don’t have a local toolshed yet... Most we have is now on a separate subversion server.... We will look in the local toolshed later. Keep you posted, Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: vrijdag 3 februari 2012 22:32 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] toolsectionlabel error (problem configuring toolshed hotplug?)
This should now be working in change set 6668:84baec18959c, which is available in our central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
[cid:image001.png@01CCE4A7.002D9380]
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
[cid:image002.png@01CCE4A7.002D9380]
On Feb 3, 2012, at 11:05 AM, Greg Von Kuster wrote:
Hi Alex,
The ToolSectionLabel element is causing the problem as it is not currently supported in the new tool shed repository installation implementation. I'll try to get a fix for this today. In the meantime, eliminating the section label from your tool config should work as a temporary workaround. I'll send you a note when I have the fix - sorry for the inconvenience.
FYI - I have a fairly complex change set coming today that will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 3, 2012, at 10:20 AM, Bossers, Alex wrote:
Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I tested thus far:
--------------------------- Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name' URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:322 in install_repository view
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
Module galaxy.web.controllers.admin_toolshed:804 in build_tool_panel_section_select_field view
options.append( ( tool_section.name, tool_section.id ) )
AttributeError: 'ToolSectionLabel' object has no attribute 'name' ---------------------------
The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to "../toolshedtools" in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy.
Any additional configs to make somewhere? In the original tool_conf.xml file?
Alex
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
Greg Von Kuster <greg@...> writes:
Hi Alex, The ToolSectionLabel element is causing the problem as it is not currently
supported in the new tool shed repository installation implementation. I'll try to get a fix for this today. In the meantime, eliminating the section label from your tool config should work as a temporary workaround. I'll send you a note when I have the fix - sorry for the inconvenience.
FYI - I have a fairly complex change set coming today that will introduce tool
versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds
can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 3, 2012, at 10:20 AM, Bossers, Alex wrote:
Somehow I seem to miss something when configuring our latest up-to-date
galaxy_central version to use the galaxy toolshed.
When as admin I want to install a tool I can browse the given 2 repositories
and select view tools.
When I select install to local galaxy it drops an error on 2 tools I tested
thus far:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name'
URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=...
Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:322 in install_repository
view
tool_panel_section_select_field = build_tool_panel_section_select_field(
trans )
Module galaxy.web.controllers.admin_toolshed:804 in
build_tool_panel_section_select_field view
options.append( ( tool_section.name, tool_section.id ) )
AttributeError: 'ToolSectionLabel' object has no attribute 'name'
The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to "../toolshedtools" in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy. Any additional configs to make somewhere? In the original tool_conf.xml file? Alex ___________________________________________________________Please keep all
replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem.
I tried hg incoming and hg pull -u to update my local instance.
Here is the result for hg summary
(galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current)
It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either.
Thanks
Lisa
Hi Lisa,
It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log?
Thanks,
Greg Von Kuster
On Mar 6, 2012, at 9:08 PM, Lisa wrote:
Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem.
I tried hg incoming and hg pull -u to update my local instance.
Here is the result for hg summary
(galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current)
It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either.
Thanks
Lisa
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:
Hi Greg, When as admin I want to install a tool from main tool shed to local galaxy,I got this error.
URL: http://128.146.132.147:1234/admin_toolshed/install_repository?tool_shed_url=... File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 322 in install_repository tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 804 in build_tool_panel_section_select_field options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name'
Your help are absolutely appreciated.
Liusong
On Wed, Mar 7, 2012 at 9:58 AM, Greg Von Kuster greg@bx.psu.edu wrote:
Hi Lisa,
It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log?
Thanks,
Greg Von Kuster
On Mar 6, 2012, at 9:08 PM, Lisa wrote:
Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem.
I tried hg incoming and hg pull -u to update my local instance.
Here is the result for hg summary
(galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current)
It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either.
Thanks
Lisa
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:
Liusong,
This problem has been corrected in our galaxy-central repository, but the fix must not yet be available in our galaxy-dist repository (which you are using). I believe a new release to the galaxy-dist repository will be available in the next few days if you want to wait for it. If not, change your ~/.hg/hgrc file so that the default path pulls from our galaxy-central repository, something like this.
[paths] default = https://<your user>@bitbucket.org/galaxy/galaxy-central
Sorry for the inconvenience,
Greg Von Kuster
On Mar 7, 2012, at 1:13 PM, Liusong Yang wrote:
Hi Greg, When as admin I want to install a tool from main tool shed to local galaxy,I got this error.
URL: http://128.146.132.147:1234/admin_toolshed/install_repository?tool_shed_url=... File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 322 in install_repository tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 804 in build_tool_panel_section_select_field options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name'
Your help are absolutely appreciated.
Liusong
On Wed, Mar 7, 2012 at 9:58 AM, Greg Von Kuster greg@bx.psu.edu wrote:
Hi Lisa,
It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log?
Thanks,
Greg Von Kuster
On Mar 6, 2012, at 9:08 PM, Lisa wrote:
Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem.
I tried hg incoming and hg pull -u to update my local instance.
Here is the result for hg summary
(galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current)
It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either.
Thanks
Lisa
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:
galaxy-dev@lists.galaxyproject.org
-
Bossers, Alex -
Greg Von Kuster -
Lisa -
Liusong Yang