Aha, that's true!
With the XML fixed, the installation dialogue changes, and displays the
"Add new tool panel section" and subsequent parts of the page.
This would *appear* to come from the check for
includes_tools_for_display_in_tool_panel on line 1620 of
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py which in turn is
(eventually) pulled from the repository model I think.
On 12/08/2014 20:03, John Chilton wrote:
> I think your tool has an XML error in it (the in_graph_filename param
> is not being closed) - I imagine this would prevent Galaxy from
> displaying the tool - cannot say if it is the only error though:
> <param format="graphml" name="in_graph_filename" type="data"
> label="Protein interaction graph"
> On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden <p...@sanbi.ac.za> wrote:
>> 1. Yes, its definitely a delete (checked the box).
>> 2. The tool, once added, creates:
>> a. the correct directory structure in shed_tools/
>> b. an entry in the tool_shed_repository table that *appears* to be correct
>> c. an entry in shed_tool_conf.xml with the annotation of the Graph
>> section (where it was originally located before being deleted
>> d. *no entry* in integrated_tool_panel.xml
>> 3. When the tool is deleted:
>> a. the shed_tools/ directory is cleaned out except for the top level
>> directory (graph_report) of the tool
>> b. the entry in the tool_shed_repository table remains
>> c. the entry in shed_tool_conf.xml remains
>> d. there is still no integrated_tool_panel.xml
>> In terms of the database, tool_version_association references
>> tool_version which references tool_shed_repository, so you need to
>> delete entries all along that chain to remove an entry from
>> The tool and its type dependency are attached.
>> On 12/08/2014 16:43, John Chilton wrote:
>>> Hey Peter,
>>> When you are deleting and reinstalling the tool - can you confirm for
>>> me that you are definitely deleting the tool and not just deactivating
>>> I don't know where to hack around from there - I think repositories
>>> are tracked in the database (tool_shed_repository) table, in
>>> shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory,
>>> tool_dependencies directory. It would be interesting to know which of
>>> these still have references to the tool after you delete it.
>>> I am also interested in the underlying bug - are you running multiple
>>> Galaxy processes? Can you send me the tool that produced this error?
>>> On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <p...@sanbi.ac.za>
>>>> Hi there
>>>> I updated a tool of mine recently, committed to the local toolshed, did
>>>> the update from within the Admin panel and then got this error:
>>>> Error - <type 'exceptions.AttributeError'>: 'Tool' object has no
>>>> attribute 'citations'
>>>> A restart of Galaxy seemed to fix the problem, but since then the tool
>>>> could not be found - it is not in any of the Tool categories. Deleting
>>>> and re-installing the tool does not fix this problem - and on
>>>> installation time I never get asked what group to add it to. It seems as
>>>> if it is somehow "stuck" in an incorrect state.
>>>> Any ideas where to go poking? Presumably there is somewhere in the
>>>> database to go poking to "reset" things.
>>>> P.S. this is with the latest Galaxy from galaxy-central.
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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: