AWS - How to reference S3 bucket from EC2 qiime2 instance

Hello,

I am with @thermokarst I think the way to go is to set up the AWS command line tools. Unless your data is public you will have to setup credentials but then you can use commands like aws s3 sync s3://bucketname/path/to/files ~/local/directory to move files from the s3 bucket to your ec2 instance

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