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_...) 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=3abd29129982504350fb7370851... 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=... 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@cancer.org.uk | +44 (0)7958 511 353
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