At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from.
This is something we're very interested in facilitating. For the long term, we're hoping to provide a structured / wiki environment for people to share tools and suites of tools, as well as providing more support in the application for adding self-contained tool suites to a Galaxy instance, injecting local configuration into tools and tool suites, et cetera. However, we'd also be very happy to see the mailing list used for this at the moment, and might even be able to open up a section of the wiki for users to list the tools they are making available.
Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist?
This is much trickier. We have to carefully consider two things when including a tool in the "default" set. 1) Quality -- we want to integrate the best possible tools for specific tasks, since one a tool starts being used, and has workflows and histories that depend on it, it is difficult to change substantially or replace. Sharing tools helps us here: if the user community comes to a consensus that a tool is useful, that is a good argument for including it upstream. 2) Security -- this is probably an even bigger concern. Tools like the "awk" tool are pretty dangerous. Until / unless the Galaxy framework can enforce complete tool isolation we definitely don't want to include a tool like this in the main distribution. -- jt James Taylor Assistant Professor Department of Biology Department of Mathematics & Computer Science Emory University