Hi again,
I have just updated Picard, and am getting a similar error with some tools from that repository when I switch to older version from tool page.
I also noticed that some tools from the Picard repo appear as multiple entries for different in the tool panel rather than selecting the different versions from the drop down.
These errors are all on tools with version dropdowns, however I don't get these errors on all of the version dropdowns, for instance I can switch to an older version of fastqc no problem.
So are the new versions of tools breaking old versions, or is there a problem with the tool panel?
Any help appreciated!!
SamToFastq:
URL: http://....../tool_runner/index
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-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 107 in __call__
return self.app( environ, start_response )
File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in handle_input
errors, params = self.__check_param_values( trans, expanded_incoming, expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in __check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in update_state
group_state = state[
input.name]
KeyError: 'single_paired_end_type'
ReorderSam:
URL: http://....../tool_runner/index
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-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 107 in __call__
return self.app( environ, start_response )
File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in handle_input
errors, params = self.__check_param_values( trans, expanded_incoming, expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in __check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in update_state
group_state = state[
input.name]
KeyError: 'source'
File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 107 in __call__
File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 90 in index
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in handle_input
errors, params = self.__check_param_values( trans, expanded_incoming, expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in __check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in update_state