Dave,
Also, when I click on:
"Get repository update"
I get the following error:
##########################################################
URL: http://galaxy.tamu.edu/admin_toolshed/check_for_updates?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 202 in check_for_updates
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'
##########################################################
Thanks
--R
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <
dave@bx.psu.edu> wrote:
> Rodolfo,
>
> In order to simplify tracking down this issue, could you provide the
> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
> revision, execute the following command in your galaxy root directory:
>
> hg id
>
> To clarify, our understanding is that you installed the ncbi_blast_plus
> repository from the main tool shed, and it installed correctly. You then
> uninstalled the repository, and it also uninstalled properly. You then
> attempted to reinstall the repository, and encountered the error message
> cited in your email.
>
> Can you
confirm the above?
>
> We further understand that the repository is stuck in the 'installing'
> state. What options are available from the popup menu next to the
> ncbi_blast_plus repository on the manage installed repositories page? If
> 'Deactivate or uninstall' is available, can you try uninstalling again, and
> see if that functions correctly?
>
> --Dave B.
>
>
> On 8/1/13 07:38:22.000, Rodolfo Aramayo 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 then tried uninstalling/reinstalling the tool
>>
>> 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
>> ___________________________________________________________
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>
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