Dave, See below.... On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Rodolfo,
Please keep the thread on the mailing list by using the "Reply all" option.
Apologies
You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency.
--Dave B.
I did and it worked well it installed Blast 2.2.26+ However there are two problems: 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text 2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following: error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: Obviously it is the installed Blast that is at fault in here Thanks --R
On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
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
fd4113962c32+ (stable)
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?
This is correct
We further understand that the repository is stuck in the 'installing' state.
YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason):
"Installed, Missing tool dependencies"
What options are available from the popup menu next to the
ncbi_blast_plus repository on the manage installed repositories page?
If I click on the little arrow, it says:
Get updates Deactivate or uninstall
'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly?
It worked!
Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory:
./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
is empty!
Should I repopulate it with the one I have in my backup??
Thanks
--Rodolfo
--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=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?
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