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Yes, CodeDeploy binds to your EC2 instance via tags. So, most preferred approach is to have a 'Name' tag on your instance and then select that instance during CodeDeploy setup.
I'm having trouble with Step 6 of your setup instructions, https://github.com/airavata-courses/TeamApex/wiki/Milestone-5-Guide-to-Setting-Up-Amazon's-CodeDeploy-Travis-Integration.
The VM that I set up and instantiated in the previous steps doesn't show up in the drop down list.
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