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My question is which version of Nginx should I install on my instances, like whether I should go with EPEL, or Amazon's own, or with 2016 Nginx?

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I would recommend you to use Amazon's own repo, and if you like a later version then consider EPEL. Ans for config, you can explicitly supply the configuration required by the server.

You can add the below script while creating an instance to get your configuration,


# Install Nginx

amazon-linux-extras install nginx1.12

# Back up existing config

mv /etc/nginx /etc/nginx-backup

# Download the configuration from S3

aws s3 cp s3://{my_bucket}/ /tmp

# Install new configuration

unzip /tmp/ -d /etc/nginx

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