Figured it out...
So to get the install to work, I had to call bundle exec compass install bootstrap
. This executes compass install bootstrap
in the context of the bundle, which includes all the gems. However, this gave rise to some more problems.
The install wrote several new bootstrap javascript files to my assets/javascripts directory. In Rails 3.2, these are automatically loaded by the asset pipeline, but in the wrong order, so in my browser console, I was getting error messages for a missing constructor and calling 'popover' on an undefined object. After digging around, the solution was just to delete all the newly generated javascript files, as they are already included by having //= require bootstrap
in application.js.