How to open a desktop application(like Nuke) through browser.
for example: RV software have a url protocol. we can use that (rvlink://).
I think this is what you're looking for:
Note that this is asking your operating system to "launch the thing registered with the requested custom browser protocol". Similarly you can have a hyperlink mailto:/// which opens the email application registered on the users computer. rvlink:/// is registered by RV as one of these custom browser protocols during it's installation.
If you want more control you would need a process running on the user's machine that you interact with. For example that's the approach shotgun's competitor ftrack took leveraging a local process they call ftrack connect (http://ftrack-connect.rtd.ftrack.com/en/0.1.17/developing/tutorial/custom_applications.html)
If you want to run something completely custom you could take a look at running your own RPC. You would initiate the registered RPC command from the web application. Check out http://www.zerorpc.io/ or https://crossbar.io/ for some more information.
Good luck!