Re: [galaxy-dev] Problem with automated install & removal with of tool with tool_data_table_conf.xml.sample
Hello Greg Thanks for the information, great to hear this is already fixed - it's totally fine for us to wait for the next release of Galaxy dist. More generally I just wanted to say I've used the automated toolshed install for other tools without a problem and think this is a brilliant feature - I really appreciate the huge effort that you guys put into Galaxy. Thanks & best wishes Peter On 23/04/12 15:24, Greg Von Kuster wrote: 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%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True HTTP/1.1" 500 - "http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True"; "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/2! 0100101 Fi refox/10.0.1" Error -: global name 'handle_sample_tool_data_table_conf_file' is not defined URL: http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&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 err
Re: [galaxy-dev] Problem with automated install & removal with of tool with tool_data_table_conf.xml.sample
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%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True > HTTP/1.1" 500 - > "http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True"; > "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20! 100101 Firefox/10.0.1" > Error - : global name > 'handle_sample_tool_data_table_conf_file' is not defined > URL: > http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&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
[galaxy-dev] Problem with automated install & removal with of tool with tool_data_table_conf.xml.sample
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%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True HTTP/1.1" 500 - "http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True"; "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20100101 Firefox/10.0.1" Error - : global name 'handle_sample_tool_data_table_conf_file' is not defined URL: http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&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 frag
