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There are many options available here but ultimately depends on how you plan to deploy the instances, eg will you use Infrastructure as code using cloudformation/terraform or some other method. All methods support using a userdata script to run commands for your bootstrap.
If using cloudformation I recommend using cfn-init to bootstrap your instances as this offers a well defined structure to the bootstrap
Another important consideration is signalling that your instances are ready within your bootstrap. You should use cfn-signal if using cloudformation or lifecycle hooks within autoscale groups so you can be sure your bootstrap has completed successfully and the instance is ready for service
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Thank you @Peter_G