Load test web server though desktop application

I am using Jmeter to load test my web application. I have already tested all actions that are performed through web interface. However I also need to test one case where web server is used to provide data to desktop application. My web server is connected to storage, where information is held and I am able to get that information through IDE or command line. Basically code dependences are ketp there and when build is performed through command line, for example, those dependences are gathered. I need to check how many users can gather those dependencies at the same time (it is not possible to do this through web interface). Is it possible to do with Jmeter (or Visual Studio)?