The problem is you have to change the Installed Interpreter path in aptana studio , by default the aptana studio takes it own version of the interpreter ie org.jruby . Make sure to change the path to your locally installed ruby environment .
In order to change it go to Windows->Preference->Ruby->Installed Interpreters
If you are working in windows Add a new environment provide
RubyVM home directory = c:\ruby
If you are working in ubuntu or any other linux platform provide
RubyVM home directory = /usr/bin
This makes all the gems ,rake to available to your aptana studio . still if doesnot work
second option would be, provide the rake path where you have installed in aptana .
In order to change it go to Windows->Preference->Ruby->Rake
provide the rake path = (your-installed-rake path )
Good luck !