Installing CocoaPods on OS X 10.11
These instructions were tested on all betas and the final release of El Capitan.
Custom GEM_HOME
This is the solution when you are receiving the "Operation not permitted" error.
$ mkdir -p $HOME/Software/ruby
$ export GEM_HOME=$HOME/Software/ruby
$ gem install cocoapods
[...]
1 gem installed
$ export PATH=$PATH:$HOME/Software/ruby/bin
$ pod --version
0.37.2