Field-programmable gate arrays (FPGAs) have shown to be quite beneficial in the cloud due to their energy-efficient application-specific acceleration. These accelerators have always been difficult to use and at cloud scale, the difficulty of managing these devices scales accordingly. We approach the challenge of managing large FPGA accelerator clusters in the cloud using abstraction layers and a new hardware stack that we call Galapagos. The hardware stack abstracts low-level details while providing flexibility in the amount of low-level access users require to reach their performance needs.