Deleting the newer 0.3 version of Bowtie fixes the problem with version 0.2.

On 18 December 2014 at 13:29, Anna Terry iseeglass@googlemail.com wrote:

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'

FastqToSam: 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: 'param_type'

On 18 December 2014 at 01:12, Anna Terry iseeglass@googlemail.com wrote:

...

Hi, I am getting an error page when I try to open the bowtie2 tool page (after selecting older version 0.2 a54de7e658f7 from drop down on version 0.3 c1ec08cb34f9 page).

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: 'params'

I can't see anything that gives me a clue where to investigate further, hopefully someone here knows? I have tried updating to latest changeset, and have restarted a few times, but still the same error.

Thanks in advance for help Anna

Okay - so there are a bunch of issues here. To me the highest priority is not being able to even load and run the old versions of the tool. I have opened a pull request with a fix for that here (https://bitbucket.org/galaxy/galaxy-central/pull-request/620/stable-dont-cho...). I would expect within a couple days it is back-ported to the latest_2014.10.06 tag of galaxy-dist.

There is also the problem of the duplicated tools. For me that goes away after one restarts Galaxy (unless the tools aren't in a tool section). Can you verify that restarting Galaxy fixes the problem or that you have installed them outside a tool section (like they aren't is a Picard section on the side or something like that). The non-grouping of non-sectioned parameters is a known issue being tracked here - https://trello.com/c/l9bjV0vT/1973-tool-grouping-doesn-t-work-outside-of-too... - I don't think it has seen much movement because we generally install tools into sections on usegalaxy.org.

The issue with some of the picard tools appearing twice is a problem but we don't really have a way to resolve it. The fully qualified id changed as part of a big update to the picard wrappers - some tools have new "owners" in the tool shed. I don't think we will change the id again - so hopefully it is not a problem going forward (and we will try to limit this problem from happening again if we can). If you don't want to uninstall the older versions that are by themselves - one fix would be to open your shed_tool_conf.xml file and add a hidden="true" tag to each - this should allow workflows and tool re-running to still work without actually causing the tool to appear in the tool panel. This is how we are planning to resolve the problem on our servers. This is less than ideal - there is more about this topic here https://github.com/galaxyproject/tools-devteam/pull/34 if you are curious.

I am very sorry about all of these problems - certainly these are all still very active development priorities (how to display multiple versions, dealing with tool lineages, etc...) and I am confident there will be improvements to all of this over the next year.

Let me know if I missed something or if there are still outstanding problems.

-John

On Thu, Dec 18, 2014 at 8:29 AM, Anna Terry iseeglass@googlemail.com wrote:

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'

FastqToSam: 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: 'param_type'

On 18 December 2014 at 01:12, Anna Terry iseeglass@googlemail.com wrote:

...

Hi, I am getting an error page when I try to open the bowtie2 tool page (after selecting older version 0.2 a54de7e658f7 from drop down on version 0.3 c1ec08cb34f9 page).

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: 'params'

I can't see anything that gives me a clue where to investigate further, hopefully someone here knows? I have tried updating to latest changeset, and have restarted a few times, but still the same error.

Thanks in advance for help Anna

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