Hello Peter, This issue was fixed a while ago, but has not yet made it to the Galaxy dist repository. Since the dist repository is generally 4 to 6 weeks behind the Galaxy central repository, your local Galaxy instance will have to track the central repository instead of the dist repository in order to use any features that interact between Galaxy and the tool shed. I believe a new release to the dist repository is scheduled for some time in the next week or so, so you can wait for it if you want.
Sorry for the inconvenience! Greg Von Kuster On Apr 23, 2012, at 5:53 AM, Peter Briggs wrote: > Hello > > I've encountered some problems installing and then trying to remove a tool > from the main toolshed in a local Galaxy production instance. The tool is the > tmap_wrapper but I don't think that the tool itself is the problem. > > When I tried the automated install from the toolshed, the Galaxy window came > back with "Server error" and in paster.log I found this: > > == paster.log fragment start == > galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,151 Installing repository > 'tmap_wrapper' > galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,186 Cloning > http://toolshed.g2.bx.psu.edu/repos/nils > homer/tmap_wrapper > galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,114 Updating cloned > repository to revision "40ade4f81a30" > galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,278 Data > table named 'tmap_indexes' is required by tool but not configured > galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,322 Adding new row (or > updating an existing row) for repository 'tmap_wrapper' in the > tool_shed_repository table. > galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,400 Data > table named 'tmap_indexes' is required by tool but not configured > 130.88.213.137 - - [20/Apr/2012:15:46:15 +0100] "POST > /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True > HTTP/1.1" 500 - > "http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True"; > "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20! 100101 Firefox/10.0.1" > Error - <type 'exceptions.NameError'>: global name > 'handle_sample_tool_data_table_conf_file' is not defined > URL: > http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in > __call__ > body = method( trans, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 173 in decorator > return func( self, trans, *args, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', > line 316 in install_repository > shed_tool_conf=shed_tool_conf ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 890 in > load_repository_contents > repository_tools_tups = handle_missing_data_table_entry( trans.app, > tool_path, sample_files, repository_tools_tups ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 753 in > handle_missing_data_table_entry > error, correction_msg = handle_sample_tool_data_table_conf_file( app, > sample_file ) > NameError: global name 'handle_sample_tool_data_table_conf_file' is not > defined > == paster.log fragment end == > > (I've replaced the machine name in the URLs with X's so our sysadmin won't > maim me.) It seems that the error is something to do with Galaxy failing to > handle the tool's tool_data_table_conf.xml.sample. > > As far as I can tell the hg clone of the tool worked okay as the files for > the tool can be found in > /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nilshomer/tmap_wrapper/40ade4f81a30/tmap_wrapper/tmap_wrapper_0.0.19 > but the tool doesn't appear in the tool panel and isn't referenced in either > the shed_tool_conf.xml or tool_conf.xml files. > > However: the tool does appear under the Admin -> Manage installed tool shed > repositories option in Galaxy. Unfortunately attempting to uninstall it via > this interface also fails with the "Server error" in the Galaxy window. This > section of paster.log looks relevant here: > > == paster.log fragment start == > Error - <type 'exceptions.TypeError'>: coercing to Unicode: need string or > buffer, NoneType found > URL: > http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=f2db41e1fa331b3e > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in > __call__ > body = method( trans, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 173 in decorator > return func( self, trans, *args, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', > line 181 in deactivate_or_uninstall_repository > remove_from_tool_panel( trans, repository, shed_tool_conf, > uninstall=remove_from_disk_checked ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 989 in > remove_from_tool_panel > tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( > trans, repository ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 490 in > generate_tool_panel_dict_from_shed_tool_conf_entries > tree = util.parse_xml( shed_tool_conf ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py', line 105 in > parse_xml > tree = ElementTree.parse(fname) > File > '/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py', > line 859 in parse > File > '/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py', > line 576 in parse > TypeError: coercing to Unicode: need string or buffer, NoneType found > == paster.log fragment end == > > After this the tool files are still there under the "shed_tools" directory, > and the tool still appears under "Manage installed tool shed repositories". > > We're using the most recent galaxy-dist (hg reports our most recent changeset > as 6799:40f1816d6857). > > I don't know if anyone else has encountered this problem but it would be > useful to know how to either complete the automated install or else be able > to remove the tool completely and add it manually for now. > > Apologies btw for the long message, thanks for your help - Galaxy is > fantastic and all the work that has gone into it is very much appreciated! > > Best wishes > > Peter > > -- > Peter Briggs peter.bri...@manchester.ac.uk > Bioinformatics Core Facility University of Manchester > B.1083 Michael Smith Bldg Tel: (0161) 2751482 > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
