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 :)


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