Hi Anne,

>From your paster log it looks like the repository is installed, but for 
>whatever reason your shed_tool_conf.xml file cannot be updated.  I've tried 
>many things, but am not able to reproduce this.  Can you answer the following?

Have you ever been able to install a tool from the tool shed, or is this your 
first attempt?

Is the tabular2html repository successfully installed on disk?

Is there a row added to the tool_shed_repository database table for the 
tabular2html repository?

What database are you using for your Galaxy instance?

What setting do you have for tool_config_file in your universe_wsgi.ini?  For 
the file to which the setting refers, can you paste its entire contents below?

Thanks!


On Jan 30, 2012, at 5:12 AM, Anne Pajon wrote:

> 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 
> http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html
> 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: 
> toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, 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 (Macinto!
 sh; 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=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&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 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 (Macin!
 tosh; 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=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&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 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.pa...@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_shed_repositories_installed_into_a_local_Galaxy_instance
>>>> 
>>>>> 
>>>>>> 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_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
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 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
>>>>>>>> g...@bx.psu.edu
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 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
>>>>>> g...@bx.psu.edu
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> --
>>>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 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
>>>> g...@bx.psu.edu
>>>> 
>>>> 
>>>> 
>>> 
>>> --
>>> 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
>>> 
>>> 
>>> 
>>> 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
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>>> 4AD.
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>> 
>>> http://lists.bx.psu.edu/
>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
> 
> --
> 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
> 
> 
> 
> 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:
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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