On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo <raram...@tamu.edu> wrote:
> People,
>
> I successfully installed NCBI_Blast_Plus from the toolshed
> The tool, however, failed to work giving the following error:
>
> Fatal error: Exit code 255 ()
> Error: NCBI C++ Exception:
>     
> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
> line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
> Attempt to access NULL pointer.

I've seen that kind of error from NCBI BLAST+ before - do you
know which of the BLAST tools was this, and what the query
was?

> I then tried uninstalling/reinstalling the tool
>

I doubt that will make any difference at all - this null pointer
exception is not a problem from Galaxy.

> However I now get an eternal 'installing' grey message and when I
> click 'manage the repo' I get:
>
> #########
>
> URL: 
> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
> File 
> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File 
> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__
>   return self.application(environ, start_response)
> File 
> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 190 in handle_request
>   body = method( trans, **kwargs )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 221 in decorator
>   return func( self, trans, *args, **kwargs )
> File 
> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 561 in manage_repository
>   repository = suc.get_installed_tool_shed_repository( trans, repository_id )
> File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
> line 515 in get_installed_tool_shed_repository
>   return trans.sa_session.query( trans.model.ToolShedRepository ).get(
> trans.security.decode_id( id ) )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
> line 60 in decode_id
>   return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
> ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'
>
> #########
>
> How can I totally uninstall and re-install this tool?
>
> Thanks

You seem to have found a bug in the Tool Shed, so thank you
for reporting this.

Peter
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