On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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?
The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser > >> 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. You are welcome But any ideas on how to properly uninstall and re-install the tool?? Thanks --R > > Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
