What I’m trying to design is a system where-by a user can upload a compiled .hex file to a web site, and then that web server sends it on to another server which has a microprocessor connected to it via USB. The web server would then trigger a script to run on that sever which would load the .hex file to the micro.
So my question is: Is it possible for a web server to trigger a shell script or C/Java program on another (trusted) machine?
Yes it’s possible. Webservers often support invocation of scripts, usually with the CGI interface. This scripts can perform the required interaction with the other server. How this has to be implemented depends on the webserver and its configuration.
If there is a microcontroller is involved and how this is connected to the second server is not related to this question. Therefore I suggest to remove the
microcontrollertag. It’s also doubful if it’s somehow related toshellat all.