Regardless of how you get inside, you'll probably want to just ghost the warehouse. The only other option is to just get into a shootout, or get creative with the stun gun and tranquilizer darts. There's a clear stealth path that you can take. If you came in the front door, make your way over to the office in the corner. You'll already be here if you came in through the roof.
From the office door, you should be able to see a clear path to the left. There are only two true patrols and there's plenty of cover. As long as you stay crouched, the men looking in the crates shouldn't notice you. That said, don't bother taking them out. It's hard to hide a body in here.
Swing to the left and walk right past the man searching in the crates. The first patrol will just walk down the center of the room, so you should never be in his line of sight. Move over to some crates on the left and then take cover. Watch the patrol here and wait for him to turn away and walk back to the center of the room. If he's walking away, you should be able to keep sticking to the left wall, and make it to the door that leads to the lobby. Move inside and shut the door.
There are two men inside. You should be able to chain up two non-lethal takedowns, or even just ignore them, since they're focused on the barricade and not you. The only thing of interest inside here is a computer that you can get a few emails off of, and a drawer with a 100-credit card on it.
Go up the steps to the office and swing the door open, then quickly take cover. Wait for the three men to split up. One will go into the locker room on the left, one will go into the break area on the right, and the last will just patrol the hallway. Wait for him to make a patrol, then move up and just take him down quietly.
You can actually just ignore the room on the right, unless you just want to keep things clear. Note that any noisy kills in here will draw in any surviving guards in the main warehouse or the lobby, so keep that in mind. The locker room guard is in a simple patrol, in a room filled with cover. It should be an easy takedown. There's a lot of ammo inside the lockers, along with a concussion grenade. Feel free to stock up.
The real objective is to turn the corner and make your way over to assembly line 1. Just do the easy hack and enter the checkpoint. Go through and wait for the decontamination to run. There's an energy bar on the floor, so grab it while you walk through. Once the doors open, just enter the new area.