On Tue, Mar 19, 2013 at 1:15 PM, Greg Von Kuster <greg@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_too...
...
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