You have a "tube shield" like the Axiris IV3 shield or the Nixie shield and you want to make a clock. You will definitely need an Arduino. You can either program it to (roughly) count the seconds, minutes, hours, or you can add an extra RTC, specialized in (accurate) time keeping, and program your Arduino to just get the time from RTC. The latter is Wiseduino, the first board I ever designed (also discontinued a long time ago). I badly needed one to finish the Axiris IV3 clock, since neither the software solution (second-counting) nor the hardware solution (adding a second RTC shield) was suitable. And so I re-designed it, improved on existing features (power, RTC) and added new ones (support for XBee/BTBee/GPSBee). This new version, spelled "wsduino" (but still pronounced "wiseduino") is shown below, next to the Axiris IV3 shield.
The wsduino board has an Arduino-compatible footprint, so it fits perfectly in the Axiris-designed-and-made enclosure (which I got as a gift from Nick :).
As you notice from the photo, the crystal is optional. Lately, I prefer to run the ATmega328 processor with the internal oscillator at 8MHz. The fewer the parts, the fewer the points of failure (and also cheaper). The wsduino board can be powered from either the USB miniB connector, or from the barrel connector, through a 7805 voltage regulator, selectable with a jumper. The board also has a 500mA 3V3 regulator, soldered on the bottom.
The DS3231 RTC is also soldered on the bottom. An XBee-footprinted serial device is connected to Rx/Tx of ATmega328, with voltage-divider level-shifting for Tx (pin D1). For the Axiris clock, I used the BTBee as a way to set the time and date, since the enclosure was not designed with buttons in mind. The sketch can be found here.
The photo below shows a couple of wsduino bare boards, top and bottom.
wsduino kit can be purchased here.