Hi Peter,

Please feel free to edit the ToolConfigSyntax page if you get a chance.  
Unfortunately I have my hands full with just the tool shed wiki, and it is not 
possible for me to get time to keep the extensive Galaxy documentation current. 
 Any help is much appreciated!

Greg Von Kuster


On Mar 19, 2013, at 9:30 AM, Peter Cock wrote:

> On Tue, Mar 19, 2013 at 1:15 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Peter,
>> 
>> You are correct.  A tool dependency definition is associated with a tool via
>> the tool config's <requirement> tag set.  The combination of name, version
>> and type is used to associated a tool with a tool dependency.  In this case,
>> the name is "blast+", the version is "2.2.26+" and the type is "package".
> 
> OK - with the rest of your email that is easily fixed then.
> 
>>> If so, then the wiki needs updating as it only describes python-module
>>> and binary as requirement types:
>>> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>> 
>> The above wiki is the wiki for Galaxy, and does not pertain to the tool
>> shed.  As mentioned above, Galaxy itself does allow for tool config
>> <requirement> tags to not include version information where the tool shed
>> does require this.
>> 
>> The tool shed wiki that describes this is available at:
>> 
>> http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
>> 
>> ...
> 
> That is a lot clearer now, but this division of tool XML features between
> "Galaxy" and the "Tool Shed" is quite unclear to me (and I think the
> current divided documentation on this point is extremely unhelpful).
> Since the ToolConfigSyntax describes how to write a tool wrapper XML
> file, I think it needs to include the "package" type under the <requirement>
> notes (and link to that bit of the ToolShedToolFeatures page). Can you
> revise that, or should I try to edit the ToolConfigSyntax page accordingly?
> That should sort out this confusion :)
> 
> Thanks,
> 
> Peter


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