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I'm trying to start a script every time I start my amazon micro instance (amazon linux ami). I tried to put it in /etc/init.d/ and linkted it to /etc/rc.d/ but the script is not executed.
I've also looked at user-data scripts, but as I understand the documentation they are only executed on the first startup of the instance.
What do I have to do to run my script on every startup?

AnonymFx
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Init.d/rc.d are primarly used for services. Any scripts that you install here have to be enabled to run at boot chkconfig service on.

Since it sounds like you are really just running a one time script. You can set it up to run with cron using the @reboot flag instead of providing a time.

datasage
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