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Reboot on a bamboo agent

I am new to bamboo , and have installed the remote agent on a linux machine to run my tasks on.

The problem i have is 

i am calling a script in my plan , that reboots the linux box the agent runs on. 

Is there any way i can handle this in bamboo? like can i just wait untill the bamboo agent comes back up without HBK detecting a hang ?

Thanks for your answers.

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