I've just uploaded a set of updates to my proteomics tools on the toolshed.  These contain my best attempt to implement automatic dependency installation ... and for the most part it seems to work. 

I have encountered the following issues though

(1) I don't see any way to ensure that one repository_dependency is installed before all others.  In my case this is important because I have an installer package (galaxy_protk) which needs to be installed before other package installs will work.

For example .. try installing

(2) Running multiple repo installs at once is not reliable (sorry this is so vague).  When I have many dependencies being installed at once I get the following error (for example)

"Could not cd to ./database/tmp/tmpbIqBW8/galaxy_protk/./database/tmp/tmp3vhKn6/galaxy_protk"

It looks like a path is not being constructed correctly. 

If I wait until the currently installed repo is finished .. then try uninstalling and reinstalling it works.

Sorry this is vague but if you try installing any of the following repositories you should see what I mean

Anyway .. and just so it doesn't just sound like I'm complaining ... I think the dependency installation stuff is hugely useful.  It took me a while to figure out all the details .. but I think it makes sense now.

Cheers

Ira