Re: [galaxy-dev] shed_tool_conf.xml not updated

Hello Anne, I apologize for the delay in responding to you on this. The first issue I see is that the revision of your local Galaxy instance implies that your repo is not being updated from the Galaxy central repository on bitbucket. Unfortunately in order to use the tool shed, you local Galaxy instance must be up to date with the central repository since the Galaxy distribution repository generally lags 6 to 8 weeks behind the central repository, and so the communication between Galaxy and the tool shed is often not functionally correct. The central repository on bitbucket is current at revision 6626:d8af2f7b1f35. For clarification what value have you set for the tool_path config setting in your shed_tool_conf.xml file? After you update your Galaxy instance, try installing the tool again and let me know if you encounter issues. Thanks very much! Greg Von Kuster On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: > Hello, > > When installing a tool from the tool shed repository into our local instance, I've got a page with "Server error". When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. > > Bellow is my previous email "server error when installing tool from tool shed repository into local instance" sent two days ago detailing what I have done and the log related to the error. > > Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. > > Let me know if you have any suggestions. > Kind regards, > Anne. > > > On 25 Jan 2012, at 16:43, Anne Pajon wrote: > >> Hello, >> >> I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. >> >> I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_to...) without success. >> >> Here is what I've done. >> >> (1) I've edited my universe_wsgi.ini >> # -- Files and directories >> >> # Tool config files, defines what tools are available in Galaxy. >> # Tools can be locally developed or installed from Galaxy tool sheds. >> tool_config_file = tool_conf.xml,shed_tool_conf.xml >> >> # Default path to the directory containing the tools defined in tool_conf.xml. >> # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. >> tool_path = tools >> >> (2) I've created the directory shed_tools/ above the galaxy-dist/ as recommended >> >> (3) I've restarted the server >> >> (4) I've logged in as "admin" user. I've clicked the "Admin" link in the top Galaxy tool panel to display the Galaxy Administration interface and then "Search and browse tool sheds" under "Tool sheds" from the left blue section to display the Accessible Galaxy tool sheds page, click "Galaxy main tool shed" to display the valid repositories and choose tabular2html and click on Install to local Galaxy, select the panel section and click Install. >> >> I get a page with "Server Error". >> >> Strangely, the tool appears in the list of tools and works in my Galaxy instance. The tool files have been installed on disk at the directory created in (2) but the shed_tool_conf.xml has not been updated. After restarting my Galaxy server, the tool is not visible anymore. >> >> Here is what appears in the log related to the installation of the tool: >> galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Installing repository 'tabular2html' >> galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html >> galaxy.util.shed_util DEBUG 2012-01-25 14:20:55,486 Updating cloned repository to revision "a5814dd5a11a" >> galaxy.tools DEBUG 2012-01-25 14:20:55,652 Reloading section: My Tools >> galaxy.tools DEBUG 2012-01-25 14:20:55,673 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0 >> .0. >> 143.65.172.178 - - [25/Jan/2012:14:20:54 +0100] "POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.ps >> u.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c6573 >> 2066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f74616275 >> 6c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True HTTP/1.1" 500 - "http://uk-cri-lbio08/galaxy/admin_toolshed/insta >> ll_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d >> 6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e >> 7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True" "Mozilla/5.0 ( >> Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13" >> Error - <type 'exceptions.TypeError'>: cannot serialize None (type NoneType) >> URL: http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_u... >> 9982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c6172206 >> 46174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c202261353 >> 8313464643561313161225d7d&includes_tools=True >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ >> app_iter = self.application(environ, start_response) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ >> return self.application(environ, start_response) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ >> return self.application(environ, start_response) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ >> body = method( trans, **kwargs ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator >> return func( self, trans, *args, **kwargs ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 275 in install_repository >> new_install=True ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 644 in load_repository_contents >> add_to_config=True ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 699 in load_altered_part_of_tool_panel >> add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 41 in add_shed_tool_conf_entry >> new_shed_tool_conf.write( util.xml_to_string( tool_panel_entry, pretty=True ) ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/__init__.py', line 113 in xml_to_string >> return ElementTree.tostring( pretty_print_xml( elem ) ) >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 1006 in tostring >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 660 in write >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 695 in _write >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 827 in _escape_a >> ttrib >> File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 774 in _raise_se >> rialization_error >> TypeError: cannot serialize None (type NoneType) >> >> Any help would be very welcome. Thanks a lot in advance. >> Kind regards, >> Anne. >> >> -- >> Anne Pajon, Ph.D. >> Cancer Research UK - Cambridge Research Institute >> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE >> anne.pajon(a)cancer.org.uk | +44 (0)7958 511 353 >> >> > > -- > Anne Pajon, Ph.D. > Cancer Research UK - Cambridge Research Institute > Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE > anne.pajon(a)cancer.org.uk | +44 (0)7958 511 353 > > > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. > > We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. > Cancer Research UK > Registered in England and Wales > Company Registered Number: 4325234. > Registered Charity Number: 1089464 and Scotland SC041666 > Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. > > ___________________________________________________________ > 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/ Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu