Hello Nikhil, On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote: Regarding this, do you mean that you have something like the following setting? tool_config_files = tool_conf.xml,shed_tool_conf.xml

To get the repositories out of the limbo state, you'll have to get into your database and run the following sql command. Doing this will allow you to install those repositories that were in limbo. After they are installed, you can uninstall them if you want to. The case on the Strings is necessary. update tool_shed_repository set status = 'New' where status = 'Cloning'; It was great to talk with you at the conference as well! Greg On Aug 3, 2012, at 8:36 PM, Nikhil Joshi wrote:

Hello Fab, What version of Galaxy are you running? Did you install it from the galaxy-dist repo on bitbucket? Am I understaning correctly that you are using a symbolic link to point your installation directory to /var/lib/galaxy-server/shed_tools? If so, why not just set the config setting to that path? From your paster log, it looks like that directory is not being used: See my inline comments for your 3 questions. On Nov 27, 2012, at 4:10 AM, fab wrote: > 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/6773... > /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 > > 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' It depends on the database you have configured in your community_wsgi.ini file. What database do you have configured there? I'm not sure to what you are referring here, so I cannot answer this. Again, I'm not sure of the solution Nikhil gave, and I don't have time to investigate it. I'm fairly certain, however, that the solution is outdated, as the features for handling installation errors have been vastly enhanced since my email exchange with him.