A chicken door - using photo illuminated sensor

@kimski 

It would be interesting if you attached an image of the sliding door you have installed and how you connected the stepper motor. Do you wind the door up with a string wrapped around the output shaft or do you have a screw drive or what?

What type of stepper motor and how powerful is it?

Stepper motors are usually used for precision positioning such as for a printer or robotic arm so unless the door is to have multiple positions,  not just up or down,  a stepper motor seems a strange choice over a cheap dc motor.

Once it is all working smoothly then I would think about the sensors or clock to control when it opens or closes.

I think you also mentioned wanting to count the chickens going in and out?