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There are some ways to do this:

1. Set up a webhook for PullRequestEvent. It sends POST request to your server with essential information about PR, so you can run builder(s) if request is received - Proper way.
2. Take a look on GitHub API. It allows you receive information about each pull requests by demand (e.g. curl https://api.github.com/repos/Itseez/opencv/pulls/604).
   So, you can periodically examine PR's statuses, and if they have been recently updated (field updated_at in response) run the builders - Tricky, but fast to implement solution.