Pictures from you,(like Ol Grey said) will help us be able to help you. Are you going to put a solid roof on your run? Also if you add your general location to your profile, it will help us know weather related issues you may have for your coop and run.
Assuming it's corrugated metal and some reasonable gauge, you can just drill some holes in it and then use self tapping screws to attach lumber furring strips to the edges you want to attach the pen to. Then you can attach the pen mesh using a pneumatic stapler or screws and washers or by layering another furring strip on top.