Easiest is to start them in a child process:
https://nodejs.org/api/child_process.html
For things with a bit of startup time, or that you will want to use frequently, start them as a daemon and send them requests as though they were an external API (using whatever protocol or socket makes sense for your tool)
Example: I made a meteor app that calls a python tool for image segmentation and background removal.
Initially, I used spawn to start the python process and perform the segmentation.
Starting the python process took 2s (loading ML models) and the segmentation took 0.35s.
So I changed the python tool to run a webserver and POSTed the file path to it instead, saving the startup time for each image and speeding up the process by a lot