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.tanger@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=f2db41e1..." "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=f2db41e1..." "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=f2db41e1..." "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=f2db41e1..." "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
Hi paul,
We'll need enough information from your paster log to determine the
On Fri, Sep 14, 2012 at 4:45 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: 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_she...
), 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?
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