From the GUI settings menu, you can set default printer options. From

I usually like printing on both sides of a piece of paper. For arcane reasons, this is called "duplexing" (a lot of printing terminology is arcane). When I buy a printer, I always try for one that can do automatic duplexing. Context: I use Fedora with Gnome and CUPS. For years now, I've been a little perplexed why my printing from GUI applications is duplex and from other applications, is single-sided. I now know more of the answer. the print dialogue box of GUI applications, you can also set this option. Page Setup: Two-sided can be One Sided Long Edge (Standard) Short Edge (flip) These options don't affect printing from non-GUI programs (eg. lpr and alpine). For that, you use the lpoption command lpoptions -o sides=two-sided-long-edge (Notice the different terminology?) It surprised me to learn that options settings are persistent. lpoptions(1) saves the setting in ~/.cups/lpoptions. Reading the lpoptions manual, I thought that it was the other way around: that a user could edit this file and lpoptions(1) would take that as a starting point. A good thing too, since the format of the file is not documented. You can also put the options on some commands directly, for example lpr(1). If root executes lpoption(1), the file /etc/cups/lpoption will record the result. Ordinary programs that are not running as root consult this file as well as ~/.cups/lpoptions It seems goofy and annoying that the two different ways of setting printer options don't communicate. Printer settings can get even more complicated when you look at ppds. I think that is because different printers have different settings.