cyclone5_handbook.pdf
Look for issue A-26 Full Configuration (p. 3800): “The HPS uses the FPGA manager to configure the FPGA portion of the device. The following sequence suggests one way for software to perform a full configuration…” Then you have to find registers with mentioned bits in the configuration flow to controll the process (find correct register offsets).
Or look here for short view Booting and Configuration Introduction
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