Organizations, such as universities, that build and operate small satellites on very limited budgets are usually unable to purchase specialized COTS tools to support mission operations due to purchase, customization, and maintenance costs.
GOTS solutions are usually old, cumbersome, and/or require customization by government agency (which is usually not cheap).
The usual solution is to cobble together software that are mission specific and designed to be just sufficient to operate the satellite and possibly ground stations using MATLAB, LabView, or other COTS software utility tools.
Develop a system of open source software applications that are designed from the start to be easily adaptable for multiple missions and to diverse operation centers. Result is the Comprehensive Open-architecture Space Mission Operations System (COSMOS) COSMOS is being developed as a collaboration between HSFL, NASA Ames Research Center, and other universities.