I am assuming you want to run an OOTB jobs via the command line.
So what I would do is wire up a process that in one of its steps it runs the job you are interested in.
Then use (C#, Java, Powershell) write a simple script/program to use the invoke action web service method:
https://cppm.ondemand.ca.com/niku/wsdl/InvokeAction/Process?tenantId=clarity
to fire off the process containing the job.
V/r,
Gene