How do I turn builder rough-in plumbing into a basement bathroom?
Given what we know (virtually nothing), the question is too broad. Order of operations depends on a number of design and product choices. Here's a rough outline.


Frame the walls. Be sure that your toilet flange is centered 12" from framing. Be sure that your other plumbing and cabinetry plans fit as expected. 
Run plumbing through the walls for your fixtures. Cap pipe stubs. 
Rough in electrical. 
Insulate and install vapor barrier as appropriate. 
Install tub or shower pan. Install shower surround if it goes against framing. 
Install drywall. Tape. Texture. Paint. 
Install flooring and cabinetry in the desired order. Depends on flooring which comes first. Ceramic tile tends to go in after cabinetry. Vinyl may go in before. 
Install trim woodwork (doors, casing, base, shoe). 
Install electrical devices and trim.
Install shower surround if it goes over drywall.