The first question is, does this board support an external trigger?
Supporting an external source providing highly accurate 1-second signals to tell the software when to capture a segment of the RF spectrum. Logic level (e.g. 3.3 V) on the rising edge.
In our case we are going to take a logic input and look for its positive rising edge. This can be done in logic. When we receive that edge, we will start capturing the sample output of the ADC and incrementing a counter. This will repeat until 85536 samples are captured. That can be also done in logic and no special type of input is required - although the Schmitt Trigger would be a good one here since the signal is coming from an external clock.
The trigger input should be edge sensitive and directly cause action - not through an interrupt or interrupt like routine. i.e. can be used directly to cause action through a short logic chain, that will be fine.
The second question is, what is the jitter spec for the external trigger?
Where jitter is the variance in time between the edge of the sample clock and the time the sample is actually taken. Jitter should be in fempto-seconds. Or listed as 0.1 pico-seconds.