I’m going to assume that you will use Mac’s native interface to make folders, copy, and move files. This primer will focus mainly on how to run perl scripts and download next gen sequence files.
To get to the command line, go to the Applications folder, than the Utilities folder. Open the program called Terminal. I recommend after opening Terminal for the first time, right-clicking (control+left click) the icon in the dock and under Options selecting Keep in Dock.