How can I get my truck to start after anti theft alarm went off?

What is your question?

If the truck sits more than a day it needs to be jummped. In this instance, while jumping tried to turn engine over the alarm system went off. Didn't even know there was an alarm system. Had to disconnect both batteries to get it to stop. Now the truck will not start. I'm thinking because of an anti theft reason. How can I get my truck to work again??