You can only use the Quartus tools which include the command line programming tool and NIOS within the supported OS as shown in the link here:
Thank you for your response. Is there any other way to program Intel FPGA from Green Hills integrity RTOS? or is it possible to get the source code of those NIOS utilities?
The Quartus tools are not open source software. Perhaps you can try to consider using the supporting OS for example Ubuntu 16.04 does support Quartus tools.