Actually, from what I understand, because the refinery will be refining at a capacity of 50,000 barrels per day, they only need permits from the state. The federal permits are required for larger projects than 50,000 barrels per day.
The federal government is NOT in charge because this is comparatively speaking, a "small" refinery having a maximum volume of 50k bpd. This project is within the jurisdiction of TCEQ.