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.