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 =
... 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 

Error Traceback:
View as:   Interactive  |  Text  |  XML (full)
⇝ IOError: [Errno 2] No such file or directory:
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/',
line 98 in __call__
File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/', 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/', line
80 in __call__
  return self.application(environ, start_response)
File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/',
line 632 in __call__
  return self.application(environ, start_response)
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/', line 160 in
  body = method( trans, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/', line 184 in
  return func( self, trans, *args, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/',
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/', line 184
  return func( self, trans, *args, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/',
634 in install_tool_shed_repositories
  reinstalling=reinstalling )
File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/',
707 in handle_repository_contents
  repository_tools_tups, sample_files_copied = handle_missing_index_file(, tool_path, sample_files, repository_tools_tups )
File '/usr/lib/galaxy-server/lib/galaxy/util/', line 1180 in
  repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ),
guid=guid )
File '/usr/lib/galaxy-server/lib/galaxy/tools/', line 437 in
  tree = util.parse_xml( config_file )
File '/usr/lib/galaxy-server/lib/galaxy/util/', line 106 in 
  tree = ElementTree.parse(fname)
line 859 in parse
line 576 in parse
IOError: [Errno 2] No such file or directory:

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

Thank you very much in advance, best regards,


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