Hello all,

during the last weeks the tool shed team did a lot of awesome work and
soon it should be possible to install meta-packages like Ira's
proteomics pipeline or the ChemicalToolBoX with a few clicks. Installing
all nested dependencies, datatypes and so on automatically.

One last problem I'm seeing is the grouping of tools in categories. If
you install all your tools via a meta package you don't have any choice
to group single tools in single categories. The same problem applies
when your repo have more than one tool that do not fit in one single

Before we had the repository dependencies features in Galaxy I shipped
example tool_conf.xml files and explained how to modify it manually.
These example files contained the tool-path with tools ID and the
categories with ID. 

What do you think about shipping such files in a repository and during
installation you offer a third choice to the user (next to, choose
category, enter new category name) ... something like "accept included
suggestions" and display them. 
Also for the installation via the API it would make installing a
completely new Galaxy flavour easy.

Any comments or ideas?


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