My alternator went out and after it was replaced my truck would start and quit

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The battery had lost its charge and when I was driving it today it told me that the battery wasn't charging and all of a sudden my stereo completely shut off. So I stopped at work, shut truck off and tried to restart. It started then, but now it will start and immediately shut off after the alternator had been changed. Could the security system be messed up in it? How do I reset the security if that's what it is.