Hi Greg,
So I looked at the the URL from the log file and it was trying to
write to a tmp directory owned by root, so that was a problem. I
traced the problem to a python function (make_tmp_directory) where it
was using the environment variable "TMPDIR", which was not defined.
So in our launch script we defined the variable and that seemed to
work. However, the repositories that I installed before fixing this
are in a limbo state. When I try to uninstall them I get that same
AttributeError below. Any ideas on how I can reset my installed
Galaxy toolshed repositories so that they are not in a limbo state?
I've included the entire traceback below:
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ AttributeError: 'NoneType' object has no attribute 'startswith'
URL:
http://optidavis.genomecenter.ucdavis.edu:8080/admin_toolshed/browse_repo...
Module weberror.evalexception.middleware:364 in respond view
> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
> environ, self.app)
Module paste.wsgilib:539 in
intercept_output view
> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
> return self.application(environ, start_response)
Module
paste.httpexceptions:632 in __call__ view
> return self.application(environ, start_response)
Module
galaxy.web.framework.base:160 in __call__ view
> body = method( trans, **kwargs )
Module
galaxy.web.framework:184 in decorator view
> return func( self, trans, *args, **kwargs )
Module
galaxy.web.controllers.admin_toolshed:356 in
browse_repositories view
> return self.deactivate_or_uninstall_repository( trans, **kwd )
Module galaxy.web.framework:184 in decorator view
> return func( self, trans, *args, **kwargs )
Module
galaxy.web.controllers.admin_toolshed:408 in
deactivate_or_uninstall_repository view
> repository_install_dir = os.path.abspath ( relative_install_dir
)
Module posixpath:343 in abspath view
> if not isabs(path):
Module posixpath:53 in isabs
view
> return s.startswith('/')
AttributeError:
'NoneType' object has no attribute 'startswith'
Any help is highly appreciated! BTW, it was really nice to get to
talk to you at the conference. :)
- Nik.
On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hello Nikhil,
On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
> Hi all,
>
> We just upgraded our local galaxy to the latest version and now I am
> trying to get automatic tool installation to work properly. I changed
> the universe_wsgi.ini file to enable the toolshed xml file,
Regarding this, do you mean that you have something like the following setting?
tool_config_files = tool_conf.xml,shed_tool_conf.xml
> I created
> a "shed_tools" directory one above the galaxy install, and restarted
> galaxy. But when I try to install a repository, I get this error as a
> popup: "Initializing repository installation failed".
From what tool shed are you trying to install Galaxy? When this pop-up is displayed, the
last line of your Galaxy paster log should be a url. If you paste that url into a browser
it will display a page that displays the entire stack trace for the exception. We'll
need to see this information in order to determine the cause of the problem.
> I tried this
> with various repositories, but I get the same error. Then when I go
> to "Manage installed tool shed repositories", all of the repositories
> I tried to install are stuck in the "Cloning" state. Finally, if I
> try to uninstall any of them, I get this error, with a traceback:
>
> AttributeError: 'NoneType' object has no attribute 'startswith'
>
> Any ideas?
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
>
http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
> ___________________________________________________________
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--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)