This guide was written for playing the game on brutal difficulty. If you are on a lower difficulty this will be easier.
For the first part of this fight go back to where you entered and the should be a small structure for you to hide behind with ammo to your left. Also make sure to have the 10% extra damage perk for energy based weapons. You should be able to see its legs giving you some safety while shooting him. He will spit out little spiders but use your secondary fire to wipe most of them out. Keep doing this until he moves and you move forward to get a checkpoint! (First one during a boss battle!)
The next section is harder but I found a trick & tactic that may help considerably. Have the perk Overcharged Pistol equipped, this pretty much insta kills most enemies and conserves ammo. Now where you enter you will see a computer terminal to your left try and crouch behind it as much as you can. Although your body pokes out quite a bit, the mech struggles to deal significant damage. The troops who spawn in this area shouldn't charge you and can pick them off after dealing with the mech. The smaller spiderbots won't even get spawned.
Next section. I found a trick to easily take him down. (Confirmation if this works would be appreciated) From the next area where you battle the mech run down the stairs and go into the far left corner. Now here I just defended myself which is pretty simple with the overcharged pistol. After a little while of dealing damage to the mech, the mech seems to either damage himself or something