Please suggest a clean(er) way of adding a user (like myself) to Shiny Server running on Ubuntu. I found this link: Setting up shiny User permissions but would like more advice on this. And I don't want to host RStudio server, just want to host Shiny server. Also can I run Tomcat along with Shiny server on the same machine?
I think you may be misunderstanding what that link is saying. You're not setting up different users for the Shiny server, you're setting up users on your computer, and managing them in such a way that you keep track of permissions for files you create on the computer. The important thing is to make sure the "shiny" user on your computer (which will be the one hosting your shiny server apps, unless you modify the default settings) has the correct permissions to access the files it will need when running those apps.
When you run a Shiny app, you won't be logged in as a user per se, rather the "shiny" user will host the computation for you, and deliver any output to you through your browser interface.
To my knowledge, unless you're using Shiny Server Pro, you won't have the ability to specify different users when using the apps (this is different to a "session", which is another topic).
When you create a shiny app, and install it (by moving it to the "/srv/shiny-server" folder), you'll need to make sure the user "shiny" on your computer has read access to that file at the very least. If your app involves reading data files from your computer, make sure the "shiny" user has read access to those too. If your app involves writing to files on our computer, make sure the "shiny" user also has write permission for those files.