based on this page : AD9361 high performance, highly integrated RF Agile Transceiver™ Linux device driver [Analog Devices Wiki] I am able to change the rx/tx gains while the arm is up by simply "echo" ing the value into the corresponding iio device. Also by changing the device tree value for ad9361 register I was able to change a lot of registers default value.
But It seems I cannot define in_voltage0_hardwaregain in the device tree.
So to summarize I need to set a default value for rx/tx gain in the manual mode. I can modify the device tree to set it to manual, but I don't know how to set a default value for in_voltage0_hardwaregain and in_voltage1_hardwaregain.