[Delphinus]

If you can get ahold of a diamond tipped hole saw you can drill glass pretty easily (as long as it's not tempered glass, which you can't drill).

It'd be much easier on yourself to empty the tank but I guess it's not a completely impossible task otherwise. Except that it will be a real pain! First of all if you're using a drill bit that requires a cutting oil (I have no idea if there are any that don't), to keep the drill bit wet you'll have to slowly pour oil over the drill bit as you drill. You'll probably end up getting some oil into the tank water as the drill comes through to the other side. I did this once and it didn't seem to harm anything in the tank but still I would have felt better if I could have avoided that.

If emptying the tank is not an option, then there are alternatives to drilling. If the idea is for an overflow you can go with an overflow box. If the idea is for a closed loop intake or output, I'd just have the pipe come up and over the aquarium wall.