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
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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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