Thanks for the reply Dave.The reinstallation process worked fine, but it gave 
couple of errors.

Initially it failed with a JavaScript alert like 'Initializing repository 
installation failed', but resulted in following database changes.

{{{
galaxydev=> select id,name,includes_datatypes, 
changeset_revision,installed_changeset_revision, update_available, deleted, 
uninstalled, dist_to_shed, ctx_rev, status, error_message from  
tool_shed_repository where name='emboss_5' order by id;
 id |   name   | includes_datatypes | changeset_revision | 
installed_changeset_revision | update_available | deleted | uninstalled | 
dist_to_shed | ctx_rev | status | error_message 
----+----------+--------------------+--------------------+------------------------------+------------------+---------+-------------+--------------+---------+--------+---------------
  3 | emboss_5 | f                  | 7334f6d0ac17       | 7334f6d0ac17         
        | f                | f       | f           | t            | 4       | 
New    | 
 28 | emboss_5 | f                  | c159a6ded912       | c159a6ded912         
        | f                | f       | f           | f            | 4       | 
New    | 
(2 rows)


}}}

It changed old tool's (id # 3) installed changeset revision and created an 
additional tool entry (id # 28). Both tools showed up in 'Manage installed 
tool-shed repositories' search with Active status (Installation status: New). 
Then I selected latest emboss_5 tool entry for installation which resulted in 
'Initializing repository installation failed' alert once again, but the 
installation was working fine under the hood. The EMBOSS tool installation 
completed without any errors, however, tools didn't get placed under any EMBOSS 
section (directly available - tool name/id appears as section). I will try 
reinstalling it again and see if it resolves the problem.

Also, can I keep old emboss_5 as it is? 

--
Shantanu


On Aug 16, 2013, at 3:43 PM, Dave Bouvier wrote:

> Shantanu,
> 
> My recommendation at this point would be to reinstall the emboss_5 repository 
> using the following procedure:
> 
> - Select "deactivate or uninstall" from the dropdown menu.
> - Check the box to uninstall.
> - When this completes, use the advanced search from the manage installed 
> repositories page to find the uninstalled repository.
> - Select "activate or reinstall" from the dropdown.
> - Proceed with the installation process.
> 
> 
>   --Dave B.
> 
> On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote:
>> 
>> The installed dependencies is failing as following query in 
>> './lib/galaxy/tools/__init__.py' isn't returning any results.
>> 
>> {{{
>> 
>> @property
>>     def tool_shed_repository( self ):
>>         # If this tool is included in an installed tool shed repository, 
>> return it.
>>         if self.tool_shed:
>>             return 
>> shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
>>  self.app,
>>                                                                              
>>                                              self.tool_shed,
>>                                                                              
>>                                              self.repository_name,
>>                                                                              
>>                                              self.repository_owner,
>>                                                                              
>>                                              
>> self.installed_changeset_revision )
>>         return None
>> 
>> 
>> }}}
>> 
>> The installed changeset revision used in this query is c159a6ded912.
>> 
>> 
>> The emboss installation on file-system has following path 
>> 'shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/7334f6d0ac17/emboss_5'.
>>  It's current Hg revision is c159a6ded912:
>> {{{
>> 
>> $ hg id
>> c159a6ded912 tip
>> 
>> }}}
>> 
>> The database has following entry for emboss:
>> 
>> {{{
>> galaxy=> select id, tool_shed, name, owner,  dist_to_shed, 
>> changeset_revision, installed_changeset_revision, ctx_rev from 
>> tool_shed_repository where id=3;
>>  id |       tool_shed        |   name   |  owner  | dist_to_shed | 
>> changeset_revision | installed_changeset_revision | ctx_rev
>> ----+------------------------+----------+---------+--------------+--------------------+------------------------------+---------
>>   3 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | t            | 
>> c159a6ded912       | 7334f6d0ac17                 | 4
>> (1 row)
>> 
>> }}}
>> 
>> So there is a mismatch between installed_changeset_revision in the database 
>> and the one being queried. I think the one used in the query is obtained 
>> from migrated_tools_conf.xml file.
>> 
>> {{{
>>               <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
>>                 <repository_name>emboss_5</repository_name>
>>                 <repository_owner>devteam</repository_owner>
>>                 
>> <installed_changeset_revision>c159a6ded912</installed_changeset_revision>    
>>             <id>toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: 
>> einverted28/5.0.0</id>
>>                 <version>5.0.0</version>
>>             </tool>
>> }}}
>> 
>> 
>> 
>> I am not sure how this mismatch happened though.
>> 
>> How do I fix this issue now? Should I update installed_changeset_revision 
>> entry in the database or migrated tool XML file or re-install emboss using 
>> tool-shed? Any help?
>> 
>> --
>> Thanks,
>> Shantanu
>> 
>> 
>> On Aug 15, 2013, at 3:33 PM, Shantanu Pavgi (Campus) wrote:
>> 
>>> 
>>> There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is 
>>> at revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool 
>>> was migrated using galaxy-dist provided migration script and later upgraded 
>>> using the admin panel interface. The job fails with 'command not found 
>>> error' which is resulting from 'Failed to build dependencies'.
>>> 
>>> Log entries:
>>> {{{
>>> galaxy.tools DEBUG 2013-08-15 15:25:16,021 Building dependency shell 
>>> command for dependency 'emboss'
>>> galaxy.tools.deps WARNING 2013-08-15 15:25:16,022 **** Base Path 
>>> ['/share/apps/galaxy/galaxydevelopstaging-tools']
>>> galaxy.tools WARNING 2013-08-15 15:25:16,024 ***** calling 
>>> self.app.toolbox.dependency_manager.find_dep with args emboss 5.0.0 package 
>>> None
>>> 
>>> }}}
>>> 
>>> Line containing asterisk were added by me during debugging.
>>> 
>>> --
>>> Thanks,
>>> Shantanu
>>> 
>>> 
>>> On Aug 15, 2013, at 3:10 PM, Björn Grüning wrote:
>>> 
>>>> Hi,
>>>> 
>>>>> Thanks for the reply Bjoern. It's installed correctly - green box. The 
>>>>> emboss entries in tool_dependency and tool_shed_repository look fine as 
>>>>> well.
>>>>> If I directly run an emboss command (e.g. antigenic) from CLI then it 
>>>>> seems to be working.
>>>> 
>>>> can you check a few things or paste the complete warning message from
>>>> Failed to resolve dependency on 'emboss'?
>>>> 
>>>> - Do you have more than one EMBOSS suite installed or showing up in your
>>>> Tool Panel?
>>>> - Which version is shown if you run some EMBOSS tools?
>>>> - I assume tool shed, or test tool shed?
>>>> - can you give us the revision number of EMBOSS that is installed?
>>>> 
>>>> Thanks,
>>>> Bjoern
>>>> 
>>>>> --
>>>>> Shantanu
>>>>> 
>>>>> On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote:
>>>>> 
>>>>>> Hi Shantanu,
>>>>>> 
>>>>>> can you have a look in the Admin menu if EMBOSS is installed correctly
>>>>>> (green) or if it failed (red)?
>>>>>> 
>>>>>> Thanks,
>>>>>> Bjoern
>>>>>> 
>>>>>>> I have migrated Emboss tool from dist to tool-shed using the migration 
>>>>>>> script and later updated it's revision. The tool was installed along 
>>>>>>> with it's dependencies, but it's failing to find them during job run.
>>>>> It's logging following  'Failed to resolve dependency on 'emboss', 
>>>>> ignoring' warning message in the log file. It seems like 
>>>>> build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' 
>>>>> is unable to get installed_tool_dependencies. I am not sure why this 
>>>>> would fail and how to resolve it. I have tried resetting tool metadata 
>>>>> several times, but that didn't help. Appreciate any help on resolving 
>>>>> this error. I am using Galaxy release_2013.06.03 revision.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Shantanu
>>>>>>> ___________________________________________________________
>>>>>>> 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/
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> 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/
>> 
>> 
>> ___________________________________________________________
>> 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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