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 category.
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? Cheers, Björn