This needs a lot of patience and time and has to be made fun for the dog. use his favorite treats to reward him for entering the run, over time increase the length of time you wish the dog to remain in the run before reward by bout 5 mins each time. use diversions such as hiding a bone in the run to keep the dog occupied. once your dog is comfortable in the run you can repeat the procedure closing the gate/ door etc for different ammounts of time rewarding with treats etc. it is important not to nurture the dogs insecurity by speaking in high pitched tones as this can actually be translated by the dog as a reward for being frightened. Only praise the behaviour you want and it should go greta and your dog will be run trained in a matter of days.