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/20100101 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_uninst... 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.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482