To compile a .map file into a .bsp you need to go through 3 steps: QBSP, LIGHT and VIS.

• QBSP will make a .bsp file. You could load that in the engine already but it would be lit full bright and might run slowly.
• LIGHT will add the lighting information to the .bsp.
• VIS will do magic and add information about what parts of the map are visible at a given position.

For more indepth information see http://www.gamers.org/dEngine/quake/Qbsp/ and http://www.visi.com/~jlowell/tqu/utils.html

Be aware that some tools might work a little different.

Since the tools were open-sourced and all the implementation details were open and public there are many different tools available. Following is an overview of up-to-date Quake map compilers and their pros and cons.