Re: [galaxy-dev] shed_tool_conf.xml not updated
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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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
Re: [galaxy-dev] shed_tool_conf.xml not updated
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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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' %
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Greg,
Please see below my inline answers to your questions.
On 30 Jan 2012, at 15:37, Greg Von Kuster wrote:
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?
This is my first attempt, I never been able to install any tools properly from
the tool shed.
Is the tabular2html repository successfully installed on disk?
Yes it is and the tool even works in Galaxy the problem starts when you restart
the server then the tool is not present in the tool menu anymore.
Is there a row added to the tool_shed_repository database table for the
tabular2html repository?
Yes and here is what I have in this table:
id |create_time|update_time | tool_shed
| name | description | owner |
changeset_revision | deleted |
metadata
| includes_datatypes | update_available |
installed_changeset_revision | uninstalled | dist_to_shed
+---+++--++++-+-++--+--+-+--
2 | 2012-01-30 09:54:42.31609 | 2012-01-30 09:54:42.316111 |
toolshed.g2.bx.psu.edu | tabular2html | Creates HTML tables from tabular data.
| ondovb | a5814dd5a11a | f | {tool_panel_section: {id:
myTools, name: My Tools, version: null}, tools: [{description: for
easier table viewing, guid:
toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, id:
tabular2HTML, name: Tabular-to-HTML, requirements: [], tests: [],
tool_config:
../shed_tools/toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/a5814dd5a11a/tabular2html/tabular2HTML.xml,
version: 1.0.0, version_string_cmd: null}]} | f | f
| a5814dd5a11a | f | f
(1 row)
What database are you using for your Galaxy instance?
I am using PostgreSQL.
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?
In the universe_wsgi.ini, I have:
tool_config_file = tool_conf.xml,shed_tool_conf.xml
shed_tool_conf.xml:
?xml version=1.0?
toolbox tool_path=../shed_tools
/toolbox
Thanks for your help.
Kind regards,
Anne.
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
Re: [galaxy-dev] shed_tool_conf.xml not updated
Anne, Thanks for all of your patience and help with this. You uncovered a problem that is very nice to have corrected. The fix is included in change set 6634:ebf72cda61e7 on our central repository. This change set will allow you to have section tags in your tool_conf.xml file that do not include version attributes. Selecting these sections to contain tools installed with a tool shed repository will now be functionally correct. Thanks again! Greg On Jan 30, 2012, at 12:08 PM, Anne Pajon wrote: Brilliant! It is working - no more server error and I now have a shed_tool_conf.xml updated: Let me know when you commit your next change set, so I will be able to test. Thanks a lot for your help. Anne. Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] shed_tool_conf.xml not updated
Greg, Thanks for your patience and help with this too! I've upgraded to ebf72cda61e7, cleaned all up (db, tool_conf.xml and shed_tool_conf.xml, file system) and restarted galaxy. The import of tabular2html works without the version attribute in the section of the tool_conf.xml file. After installing, I've restarted again and all is working fine as expected. Thanks for the fix. I've also tested the installation of bedtools into a new tool panel section and it works fine too but I think it has never been an issue. Thanks again. Kind regards, Anne. On 30 Jan 2012, at 17:46, Greg Von Kuster wrote: Anne, Thanks for all of your patience and help with this. You uncovered a problem that is very nice to have corrected. The fix is included in change set 6634:ebf72cda61e7 on our central repository. This change set will allow you to have section tags in your tool_conf.xml file that do not include version attributes. Selecting these sections to contain tools installed with a tool shed repository will now be functionally correct. Thanks again! Greg On Jan 30, 2012, at 12:08 PM, Anne Pajon wrote: Brilliant! It is working - no more server error and I now have a shed_tool_conf.xml updated: Let me know when you commit your next change set, so I will be able to test. Thanks a lot for your help. Anne. 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/
Re: [galaxy-dev] shed_tool_conf.xml not updated
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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c6573 2066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f74616275 6c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/insta ll_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d 6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e
Re: [galaxy-dev] shed_tool_conf.xml not updated
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
Re: [galaxy-dev] shed_tool_conf.xml not updated
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
Re: [galaxy-dev] shed_tool_conf.xml not updated
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. 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. 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
Re: [galaxy-dev] shed_tool_conf.xml not updated
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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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
Re: [galaxy-dev] shed_tool_conf.xml not updated
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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_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
