Can I generate a script to compile simulation libraries?

To generate a script to compile all the required Quartus® II simulation library files with all the correct compilation options, use the following command:

quartus_sh --simlib_comp -tool <simulation tool name> -family <device family>
  -language <language> -gen_only -cmd_file <file_name>

For example, to create a script to compile Cyclone® IV E VHDL libraries for the QuestaSim simulation tool:

quartus_sh --simlib_comp -tool questasim -family cycloneive -language vhdl -gen_only
  -cmd_file build_altera_sim.do

For further information on the quartus_sh --simlib_comp command, refer to Preparing for EDA Simulation in Quartus II Help