If you don't want to use the Arduino IDE to build an Arduino .ino file you can use the arduino-builder to integrate with a better IDE like IDEA, Eclipse, KDevelop, etc...

The command to build a project for the teensy 3.2 board is:

$arduino-builder -hardware hardware -tools tools -tools tools-builder -libraries /home/<user>/Arduino/libraries -fqbn teensy:avr:teensy31 /path/to/your/project.ino

Note: This assumes the working directory you're in is the folder where arduino is installed.

I also had to edit the hardware/teensy/avr/boards.txt and add

teensy31.build.fcpu=96000000
teensy31.build.flags.ldspecs=
teensy31.build.keylayout=US_ENGLISH
teensy31.build.usbtype=USB_SERIAL

You can find the available values for fcpu, ldspecs, keylayout, etc.. by looking at the menu option specifications in build.txt.

This is just for my own reference, you can see the great article arduino-build-errors a more detailed explaination and some other possible errors and solutions.

Happy coding!