The installed dependencies is failing as following query in
'./lib/galaxy/tools/__init__.py' isn't returning any results.
def tool_shed_repository( self ):
# If this tool is included in an installed tool shed repository, return
The installed changeset revision used in this query is c159a6ded912.
The emboss installation on file-system has following path
It's current Hg revision is c159a6ded912:
$ hg id
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
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
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?
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
> 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
> Line containing asterisk were added by me during debugging.
> On Aug 15, 2013, at 3:10 PM, Björn Grüning wrote:
>>> Thanks for the reply Bjoern. It's installed correctly - green box. The
>>> emboss entries in tool_dependency and tool_shed_repository look fine as
>>> 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?
>>> 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)?
>>>>> 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.
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> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: