ok, I forgot to set a directory for the tool dependencies in the new
install, and once I did that it worked!

On Fri, Sep 14, 2012 at 11:58 AM, Paul Tanger <paul.tan...@colostate.edu>wrote:

> *Not sure if this is what you need, but here is the info from the error
> page.  I obscured part of the IP address.*
>
>
> URL:
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=f2db41e1fa331b3e
> 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
> 184 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py',
> line 350 in browse_repositories
>   return self.reselect_tool_panel_section( trans, **kwd )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
> 184 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py',
> line 1352 in reselect_tool_panel_section
>   status=status )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
> 746 in fill_template
>   return self.fill_template_mako( filename, **kwargs )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
> 757 in fill_template_mako
>   return template.render( **data )
> File
> '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line
> 296 in render
>   return runtime._render(self, self.callable_, args, data)
> File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
> line 660 in _render
>   **_kwargs_for_callable(callable_, data))
> File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
> line 692 in _render_context
>   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
> line 718 in _exec_template
>   callable_(context, *args, **kwargs)
> File '/home/galaxy/galaxy-dist/database/compiled_templates/base.mako.py',
> line 42 in render_body
>   __M_writer(unicode(next.body()))
> File
> '/home/galaxy/galaxy-dist/database/compiled_templates/admin/tool_shed_repository/
> reselect_tool_panel_section.mako.py', line 76 in render_body
>   __M_writer(unicode(render_tool_dependency_section(
> install_tool_dependencies_check_box, [ repo_info_dict ] )))
> File
> '/home/galaxy/galaxy-dist/database/compiled_templates/admin/tool_shed_repository/
> common.mako.py', line 204 in render_render_tool_dependency_section
>   changeset_revision )
> File '/usr/lib64/python2.6/posixpath.py', line 67 in join
>   elif path == '' or path.endswith('/'):
>
> AttributeError: 'NoneType' object has no attribute 'endswith'
>
> *here is the info from the paster.log
> *
>
> 129.XX.XX.XX - - [14/Sep/2012:11:42:50 -0700] "GET / HTTP/1.1" 200 - "-"
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:42:51 -0700] "GET /root/tool_menu
> HTTP/1.1" 200 - "http://129.XX.XX.XX:8888/"; "Mozilla/5.0 (Windows NT 6.1;
> WOW64) AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89
> Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:42:51 -0700] "GET /history HTTP/1.1" 200
> - "http://129.XX.XX.XX:8888/"; "Mozilla/5.0 (Windows NT 6.1; WOW64)
> AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:42:53 -0700] "POST /root/user_get_usage
> HTTP/1.1" 200 - "http://129.XX.XX.XX:8888/history"; "Mozilla/5.0 (Windows
> NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89
> Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:42:58 -0700] "GET /admin HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/"; "Mozilla/5.0 (Windows NT 6.1; WOW64)
> AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:42:59 -0700] "GET
> /admin/center?status=done&message=&webapp=galaxy HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin"; "Mozilla/5.0 (Windows NT 6.1; WOW64)
> AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:02 -0700] "GET
> /admin_toolshed/browse_repositories HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin"; "Mozilla/5.0 (Windows NT 6.1; WOW64)
> AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:05 -0700] "GET
> /admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&
> HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories"; "Mozilla/5.0
> (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:07 -0700] "GET
> /admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=manage_repository&id=f2db41e1fa331b3e&
> HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:21 -0700] "GET
> /admin_toolshed/manage_tool_dependencies?id=f2db41e1fa331b3e HTTP/1.1" 200
> - "
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=manage_repository&id=f2db41e1fa331b3e&";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:25 -0700] "POST
> /admin_toolshed/tool_dependency_status_updates HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/manage_tool_dependencies?id=f2db41e1fa331b3e";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:28 -0700] "POST
> /admin_toolshed/tool_dependency_status_updates HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/manage_tool_dependencies?id=f2db41e1fa331b3e";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:31 -0700] "POST
> /admin_toolshed/tool_dependency_status_updates HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/manage_tool_dependencies?id=f2db41e1fa331b3e";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:31 -0700] "GET
> /admin_toolshed/manage_tool_dependencies?sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=install&id=f2db41e1fa331b3e&
> HTTP/1.1" 500 - "
> http://129.XX.XX.XX:8888/admin_toolshed/manage_tool_dependencies?id=f2db41e1fa331b3e";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> Debug at: http://129.XX.XX.XX:8888/_debug/view/1347593185
> 129.XX.XX.XX - - [14/Sep/2012:11:43:38 -0700] "GET
> /admin_toolshed/browse_repositories HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin"; "Mozilla/5.0 (Windows NT 6.1; WOW64)
> AppleWebKit/537.1 (KHTML, like Gecko) Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:44 -0700] "GET
> /admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&
> HTTP/1.1" 200 - "
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories"; "Mozilla/5.0
> (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> 129.XX.XX.XX - - [14/Sep/2012:11:43:48 -0700] "GET
> /admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=f2db41e1fa331b3e
> HTTP/1.1" 500 - "
> http://129.XX.XX.XX:8888/admin_toolshed/browse_repositories?f-deleted=True&sort=name&show_item_checkboxes=false&async=false&page=1&";
> "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.1 (KHTML, like Gecko)
> Chrome/21.0.1180.89 Safari/537.1"
> Debug at: http://129.XX.XX.XX:8888/_debug/view/1347593186
>
>
>
> On Fri, Sep 14, 2012 at 4:45 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> > Hi paul,
> >
> > We'll need enough information from your paster log to determine the
> problem.  If your server threw an exception, you may also have a stack
> trace in your browser window and we'll need that infomration as well.
> >
> > Thanks,
> >
> > Greg Von Kuster
> >
> > On Sep 13, 2012, at 10:38 PM, Paul Tanger wrote:
> >
> >> So I successfully added the emboss tools to galaxy, but I failed to
> >> create a tool panel section for them.
> >> So I thought I would uninstall them and install them again, this time
> >> creating a tool panel section.
> >> I'm following the instructions here (
> >>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_shed_repositories_installed_into_a_local_Galaxy_instance
> >> ), but I'm getting this error when trying to reinstall the tool
> >> repository:
> >>
> >> AttributeError: 'NoneType' object has no attribute 'endswith'
> >>
> >> Any ideas what I should do to get this reinstalled?
> >>
> >> Thanks!
> >> ___________________________________________________________
> >> 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/
> >
>
>
>
> --
>
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