Unfortunately they don't have PSoC Programmer for Linux. They have Cypress Programmer, but I am not sure that this will do the work. Also it looks like it's GUI based and my Linux board is all command line.
Do you mean the downloaded PSoC Prammer for Linux is Cypress Programmer?
For Linux board with all command line......I know there is COM or CLI for windows, not sure if the programmer has similar drivers on linux...
We do not have Linux compatible version of PSoC Programmer. You will have to go with bootloader implementation and design a bootloader host application on Linux.