Cocoa Pods not updating pods on El Capitan

I've upgraded to El Capitan and since then I can't update my pods.

$ pod update
-bash: pod: command not found

So I've tried to reinstall CocoaPods and got this:

$ sudo gem install cocoapods
ERROR:  While executing gem ... (Errno::EPERM)
    Operation not permitted - /usr/bin/xcodeproj

I am the administrator on this computer. Why is this happening?

This is caused by the new System integrity protection feature introduced in El Capitan. It restricts even administrators from writing to /usr/bin.

Your best option would be to install gems without needing sudo. There is a good guide on how to do that:

export GEM_HOME=$HOME/.gem
export PATH=$GEM_HOME/bin:$PATH

gem install cocoapods

From CocoaPods issues 3736

1. Uninstall all instances of cocopods (just to be safe and keep things clean) see fully uninstall Cocoapods

   sudo gem uninstall cocoapods
   

   or even better fully uninstall all components (and select All versions for each)

   gem list --local | grep cocoapods | awk '{print $1}' | xargs sudo gem uninstall
   

2. Install again

   sudo gem install -n /usr/local/bin cocoapods
   

3. Change access permission

   sudo chmod +rx /usr/local/bin/