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
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