Dave,

See below....

On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier <d...@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 <d...@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=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
>>>> ___________________________________________________________
>>>> 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/
>>>>
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>>>>     http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>
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