It just so happens that I've written a blog post on this very topic. The short answer is, in your terminal: cat tmp/codeship_projectname.pub | ssh root @dokkuinstance .com "sudo sshcommand acl-add dokku codeship_projectname" #!/bin/sh git fetch --unshallow || true git fetch origin "+refs/heads/*:refs/remotes/origin/*" # checkout a remote branch with # git checkout -b test origin/test git remote add dokku dokku@dokkuinstance.com:projectname git push dokku master Here's the full tutorial on CONTINUOUS DEPLOYMENT WITH CODESHIP AND DOKKU http://blog.sethbergman.com/continuous-deployment-with-codeship-and-dokku/