Real Time Application on myRio

Hello,  I have just started using Labview FPGA for a student project and have come across a small problem that I haven't found addressed here already: when I attempt to deploy a VI as a real time application, the source file is either unavailable or the DIO lines disconnect. I am using Labview 2016 and a myRio-1900. I'm not sure if this is a hardware or software question, sorry if this is the wrong place. 

I have written a simple code that produce a series of timed pulses used for triggering a MOSFET. Running from the project menu (under the chassis dropdown) the VI runs as desired (outputting pulses to the connector c DIO ports of the myRio). However, I would like to be able deploy the VI as a startup Real Time application, so that I can trigger the MOSFET using the myRio in situ, without access to a computer. 

I have looked at the tutorials on the process but they don't appear to come across the issue I've had. If I create a real time application and attempt to build it, the VI is not shown in the source files section (pictured). If I instead create the VI again from the higher tier in the dropdown (the NI myRio line) then the source file becomes available but the DIO ports are unavailable (greyed out) and the wires are broken. This makes sense as it's clearly not on the FPGA target, but where then is the VI meant to be selected from? How do I create a real time application with access to the DIO ports? 

Any help would be greatly appreciated.

Thanks,

Max Will