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Very Confused about setting system clock

Hi Guys,

I am very confused how to setup the system clocks without using HAL, I wrote routines that should set the clock selection as I wanted to find that the clocks were all locked. Further investigation showed that they get set in system_stm32l1xx.c, a file that was pre-generated when the project was setup and said to be configured using "STM32L1xx_Clock_Configuration_V1.1.0.xls".
I can find no reference to this tool anywhere other than in the header.

Are your meant to modify the systemInit() function to fit the requirements (dangerous should they be a update that rebuilds it)?
Does everyone use HAL to set the system clocks?

How do you get the clock setup you want, I really don't want to use HAL as it doesn't meet the safety standards I require (too much redundant code for example)

Thanks for any help
Robert