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_tool_shed_repository_tools_into_a_local_Galaxy_instance)
>  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_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd2912
> 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.pa...@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.pa...@cancer.org.uk | +44 (0)7958 511 353



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