Hi Greg,
Thanks for your answer.
I've deleted the row in the tool_shed_repository table, removed the installed tool
shed repository from disk, updated my Galaxy instance to 6629:cb458aca542e from Galaxy
central and restarted Galaxy server.
I am sorry to say but I do still have the same problem (Server Error when installing and
shed_tool_conf.xml not updated). Any ideas on why it does not work? Thanks to let me
know.
Here is my log:
galaxy.util.shed_util DEBUG 2012-01-30 09:54:40,555 Installing repository
'tabular2html'
galaxy.util.shed_util DEBUG 2012-01-30 09:54:40,556 Cloning
galaxy.util.shed_util DEBUG 2012-01-30 09:54:42,165 Updating cloned repository to revision
"a5814dd5a11a"
galaxy.util.shed_util DEBUG 2012-01-30 09:54:42,308 Adding new row (or updating an
existing row) for repository 'tabular2html' in the tool_shed_repository table.
galaxy.tools DEBUG 2012-01-30 09:54:42,376 Reloading section: My Tools
galaxy.tools DEBUG 2012-01-30 09:54:42,404 Loaded tool id:
, version: 1.0.0.
143.65.172.178 - - [30/Jan/2012:09:54:40 +0100] "POST
/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True
HTTP/1.1" 500 -
"http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&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:
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 284 in install_repository
dist_to_shed=False )
File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py',
line 649 in load_repository_contents
uninstall=False )
File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py',
line 782 in alter_tool_panel
config_elems_to_xml_file( app, shed_tool_conf_dict )
File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py',
line 25 in config_elems_to_xml_file
os.write( fd, '%s' % util.xml_to_string( elem, 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_attrib
File
'/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py',
line 774 in _raise_serialization_error
TypeError: cannot serialize None (type NoneType)
Kind regards,
Anne.
On 27 Jan 2012, at 19:38, Greg Von Kuster wrote:
Hi Anne,
OK, the only other thing this could be is that the metadata column in the
tool_shed_repository database table for this repository got corrupted during the initial
install when the revision of your Galaxy instance was not up to date. So, if the
repository once again got installed on disk, but the entry for the tool didn't make it
into shed_tool_conf,xml, then manually remove the repository from disk again. Then either
update the metadata column in the tool shed repository table for this repository to be
null or delete the record from the table.
If you're using postgres, then the update statement would be something like:
update tool_shed_repository set metadata = null where id = <whatever the id is of the
tabular2html tool shed repository>
You could also delete this record from the table and it will be recreated when you
install the repository.
After taking these 2 steps, you should be able to install the tool with no problem.
However, if there is an entry in your shed_tool_conf.xml file, remove it manually before
attempting to reinstall.
Sorry for all of this, but once you have your environment cleared up (following the steps
above) and you're running the correct change set, installing from the tool shed should
not cause you problems.
Let me know how this goes.
Greg Von Kuster
On Jan 27, 2012, at 2:27 PM, Anne Pajon wrote:
> Hi Greg,
>
> Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 from
Galaxy central repository.
>
> I tried again to install tabular2html from the tool shed, but I get the same problem
(Server Error when installing and shed_tool_conf.xml not updated). Here is my log in case
it helps.
>
> galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Installing repository
'tabular2html'
> galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Cloning
http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html
> galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,839 Updating cloned repository to
revision "a5814dd5a11a"
> galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,982 Adding new row (or updating an
existing row) for repository 'tabular2html' in the tool_shed_repository table.
> galaxy.tools DEBUG 2012-01-27 19:20:54,050 Reloading section: My Tools
> galaxy.tools DEBUG 2012-01-27 19:20:54,078 Loaded tool id:
toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0.0.
> 143.65.172.178 - - [27/Jan/2012:19:20:52 +0100] "POST
/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True
HTTP/1.1" 500 -
"http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&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...
> 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 284 in install_repository
> dist_to_shed=False )
> File
'/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 649
in load_repository_contents
> uninstall=False )
> File
'/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 782
in alter_tool_panel
> config_elems_to_xml_file( app, shed_tool_conf_dict )
> File
'/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 25
in config_elems_to_xml_file
> os.write( fd, '%s' % util.xml_to_string( elem, 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_attrib
> File
'/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py',
line 774 in _raise_serialization_error
> TypeError: cannot serialize None (type NoneType)
>
>
> CGI Variables
> -------------
> CONTENT_LENGTH: '-1'
> CONTENT_TYPE: 'application/x-www-form-urlencoded'
> HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7'
> HTTP_ACCEPT_ENCODING: 'gzip,deflate'
> HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=0.5'
> HTTP_CONNECTION: 'Keep-Alive'
> HTTP_COOKIE:
'galaxysession=c6ca0ddb55be603aa515e6fea2e6b40cf5afc201038ba85081133d60514acdbf77c49debb2b2d1be'
> HTTP_HOST: 'uk-cri-lbio08'
> HTTP_MAX_FORWARDS: '10'
> HTTP_REFERER:
'http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True'
> HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB;
rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13'
> PATH_INFO: '/admin_toolshed/install_repository'
> QUERY_STRING:
'tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True'
> REMOTE_ADDR: '143.65.172.178'
> REQUEST_METHOD: 'POST'
> SCRIPT_NAME: '/galaxy'
> SERVER_NAME: 'uk-cri-lbio08.crnet.org'
> SERVER_PORT: '8080'
> SERVER_PROTOCOL: 'HTTP/1.1'
>
>
> Configuration
> -------------
> __file__: '/opt/local/home/webapp/galaxy/galaxy-dist/universe_wsgi.ini'
> admin_users: 'anne.pajon(a)cancer.org.uk'
> brand: 'CRUK-CRI:test'
> cookie_path: '/galaxy'
> database_connection: 'postgres://galaxy:galaxy@localhost:5432/galaxy'
> debug: 'False'
> enable_tracks: 'True'
> file_path: '/data_ls/galaxy/data/files'
> here: '/opt/local/home/webapp/galaxy/galaxy-dist'
> len_file_path: 'tool-data/shared/ucsc/chrom'
> logo_url: '/galaxy'
> new_file_path: '/data_ls/galaxy/data/tmp'
> nglims_config_file: 'tool-data/nglims.yaml'
> static_cache_time: '360'
> static_dir: '/opt/local/home/webapp/galaxy/galaxy-dist/static/'
> static_enabled: 'True'
> static_favicon_dir:
'/opt/local/home/webapp/galaxy/galaxy-dist/static/favicon.ico'
> static_images_dir: '/opt/local/home/webapp/galaxy/galaxy-dist/static/images'
> static_robots_txt:
'/opt/local/home/webapp/galaxy/galaxy-dist/static/robots.txt'
> static_scripts_dir:
'/opt/local/home/webapp/galaxy/galaxy-dist/static/scripts/'
> static_style_dir:
'/opt/local/home/webapp/galaxy/galaxy-dist/static/june_2007_style/blue'
> tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
> tool_path: 'tools'
> use_interactive: 'False'
> use_nglims: 'False'
>
>
> WSGI Variables
> --------------
> application: <paste.recursive.RecursiveMiddleware object at 0xf69c910>
> paste.cookies: (<SimpleCookie:
galaxysession='c6ca0ddb55be603aa515e6fea2e6b40cf5afc201038ba85081133d60514acdbf77c49debb2b2d1be'>,
'galaxysession=c6ca0ddb55be603aa515e6fea2e6b40cf5afc201038ba85081133d60514acdbf77c49debb2b2d1be')
> paste.expected_exceptions: [<class
'paste.httpexceptions.HTTPException'>]
> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
0xf69c3d0>
> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xa3e3990>
> paste.parsed_querystring: ([('tool_shed_url',
'http://toolshed.g2.bx.psu.edu'), ('repo_info_dict',
'3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d'),
('includes_tools', 'True')],
'tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True')
> paste.recursive.forward: <paste.recursive.Forwarder from /galaxy>
> paste.recursive.include: <paste.recursive.Includer from /galaxy>
> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
/galaxy>
> paste.recursive.script_name: '/galaxy'
> paste.throw_errors: True
> webob._parsed_post_vars: (MultiDict([('shed_tool_conf',
'shed_tool_conf.xml'), ('new_tool_panel_section', ''),
('tool_panel_section', 'myTools'),
('select_tool_panel_section_button', 'Install')]), <FakeCGIBody at
e9c2350 viewing MultiDict([('sh...l')])>)
> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
'http://toolshed.g2.bx.psu.edu'), ('repo_info_dict',
'3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d'),
('includes_tools', 'True')]),
'tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True')
> wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
> Kind regards,
> Anne.
>
>
> On 27 Jan 2012, at 15:55, Greg Von Kuster wrote:
>
>> Hi Anne, see my inline comments.
>>
>> On Jan 27, 2012, at 10:26 AM, Anne Pajon wrote:
>>
>>> Hi Greg,
>>>
>>> Thanks a lot. I have the impression from what I read on the wiki that Galaxy
will be using the tool shed to provide more flexibility in choosing tools instead of
having them bundle in the current distribution. We are very much interested by these new
features because we only use a subset of the available tools plus some that we have
developed in house.
>>
>> Yes, this is correct. At some point, a subset of the tools currently in the
Galaxy distribution will be moved to the main Galaxy tool shed from which they can be
easily installed using Galaxy's new installation manager. You'll be able to very
easily install any portion of the tools that will be eliminated from the distribution.
All of this is now functional in the latest version of Galaxy as well as the main Galaxy
tool shed, but the timeline for beginning to eliminate tools from the distribution is yet
to be determined.
>>
>> The tip of the central repository, which will be added to the Galaxy distribution
repository today, includes the ability to deactivate or uninstall repositories that
you've installed from the tool shed, enabling much more flexibility in managing the
tools that are included in your Galaxy tool panel. The last section of the tool shed wiki
describes this new feature set:
>>
>>
http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_...
>>
>>>
>>>> From what you are saying, I have the impression that I will be better of
running my Galaxy instance against the central repository instead of the distribution one
if I do not want to wait for bug fixes. Am I right of thinking that? If so, I will migrate
to the central repository and let you know how it goes.
>>
>> Although this is not ideal, it is unfortunately necessary at least for the
current time. At some point, the communication layers between Galaxy and the tool shed
will stabilize to the point that the distribution repository can be used, but in the
meantime, the central repository is required. My advice for now would be to have your
Galaxy instance track central, but not necessarily update it all of the time. I believe
the update to the distribution going out today will be change set 6621:26920e20157f, which
includes all new tool shed features. So although this is not the latest on the central
repo, you can update to that revision if you want. To do so, change your hgrc to pull
from Galaxy central and use the following.
>>
>> hg pull -u 26920e20157f
>>
>> If you are comfortable in updating to the latest from central, just use
>>
>> hg pull -u
>>
>>>
>>> Before migrating and updating I will manually remove the installed tool shed
repository from disk as you advised.
>>>
>>> Kind regards,
>>> Anne.
>>>
>>>
>>> On 27 Jan 2012, at 14:57, Greg Von Kuster wrote:
>>>
>>>> Hi Anne,
>>>>
>>>> A new update to the Galaxy distribution repository is planned for today,
I believe, so unless that changes you should be able to update your Galaxy instance either
today or Monday using the distribution repository. However, this problem will continue to
exist between Galaxy instances that track the distribution repository and that also want
to take advantage of the Galaxy tool shed features that enable direct interaction between
Galaxy and the tool shed. The tool shed features are implement much more rapidly than the
Galaxy distribution is updated, resulting in this ongoing problem.
>>>>
>>>> Regarding the state of your local instance and the tool shed repository
you attempted to install - if I understand correctly, the repository was successfully
installed on disk, but the XML tag set entry for the contained tool was not added to your
shed_tool_conf.xml file. If this is the case, then you'll need to manually remove the
installed tool shed repository from disk before you try installing it again after updating
your Galaxy instance to the new upcoming distribution.
>>>>
>>>> Sorry for the inconvenience.
>>>>
>>>> Greg
>>>>
>>>> On Jan 27, 2012, at 9:35 AM, Anne Pajon wrote:
>>>>
>>>>> Hello Greg,
>>>>>
>>>>> Thanks a lot for your answer and sorry for having sent two emails.
>>>>>
>>>>> Regarding the version of our local instance, I understand perfectly
that the Galaxy distribution repository is behind the Galaxy central repository but we
would like to use Galaxy on a production server and we are looking at stable releases not
development ones. What would you advice us to do?
>>>>>
>>>>> Here is the value for tool_path in my shed_tool_conf.xml:
>>>>> <?xml version="1.0"?>
>>>>> <toolbox tool_path="../shed_tools">
>>>>> </toolbox>
>>>>>
>>>>> I'm waiting your advice to migrate my repository from Galaxy
distribution to Galaxy central. Thanks in advance.
>>>>>
>>>>> Kind regards,
>>>>> Anne.
>>>>>
>>>>>
>>>>> On 27 Jan 2012, at 13:03, Greg Von Kuster wrote:
>>>>>
>>>>>> 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
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>>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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.
>>>>>
>>>>
>>>> Greg Von Kuster
>>>> Galaxy Development Team
>>>> greg(a)bx.psu.edu
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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
>>
>>
>>
>
> --
> 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
--
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.