Help with my work out plan

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So my friend took me to a weekly PT that future marines do, since I showed interest into maybe going into the military. I learned that I was pretty out of shape!
I need advice on a good workout regimen with maybe some weights and how to build my endurance for running up! I can do spin classes no problem, but I can't run to save my life! I also have practically no upper body strength!
I'm not looking into a crazy weight loss plan, I'm not terribly overweight, I mainly want to build muscle and increase my endurance. I wouldn't mind losing fat along the way though :P
FYI: I do work at a HUGE gym! So I have access to a ton of equipment.
Thanks :)

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