Dear Greg and Nikhil, We just installed a local instance of galaxy and encountered the same problem as Nikhil for the tools we tried to install from toolshed. Unfortunately I am not skilled as you are and didn't manage to solve the problem from the information in your posts.
In my case I have in the univers_wgi.ini file: tool_config_file = tool_conf.xml,shed_tool_conf.xml ... with, in my main galaxy installation directory, a shed_tools link to the directory /var/lib/galaxy-server/shed_tools The problem is that when I try to install a tool from toolshed, it shows me the popup with "Initializing repository installation failed" and after that the tool stays in the cloning state for ever. When I try to uninstall it shows me the following message with traceback: AttributeError: 'NoneType' object has no attribute 'startswith' The entire stack trace for the exception I get just after the popup is as follow: Error Traceback: View as: Interactive | Text | XML (full) ⇝ IOError: [Errno 2] No such file or directory: u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 /beast/beast/beast.xml' URL: http://192.167.142.244:8080/admin_toolshed/manage_repositories File '/usr/lib/galaxy-server/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception /middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 846 in manage_repositories self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 634 in install_tool_shed_repositories reinstalling=reinstalling ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 707 in handle_repository_contents repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups ) File '/usr/lib/galaxy-server/lib/galaxy/util/shed_util.py', line 1180 in handle_missing_index_file repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) File '/usr/lib/galaxy-server/lib/galaxy/tools/__init__.py', line 437 in load_tool tree = util.parse_xml( config_file ) File '/usr/lib/galaxy-server/lib/galaxy/util/__init__.py', line 106 in parse_xml tree = ElementTree.parse(fname) File '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree /ElementTree.py', line 859 in parse File '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree /ElementTree.py', line 576 in parse IOError: [Errno 2] No such file or directory: u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 /beast/beast/beast.xml' I didn't manage to understand what is the original error to see if the problem is the exact same as for Nikhil. Therefore I have three questions: - how do I get in the database to run the following command: update tool_shed_repository set status = 'New' where status = 'Cloning' - how do I check for the problem that Nikhil underpinned (the python function with environment variable TMPDIR undefined)? - how do I implement the solution Nikhil gave in the case I see it is the same problem? Thank you very much in advance, best regards, fab. ___________________________________________________________ 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/
