On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raramayo@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:
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URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990... 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