You can do most/all/more of what the calibre GUI provides, using calibre's console commands.
You can use the scripting tools that are available for your operating system, For OS/X Applescript comes mind, several other are mentioned in here
http://stackoverflow.com/questions/1...6-applications
Some Calibre users don't use the GUI at all, they use the cli interface exclusively. They access the cli commands via bash scripts and even .bat files, and that's where their workflow automation is expressed.
BR