Step 4: Upload sequencing data to your S3 bucket

The AWS command line interface (CLI) installed in step 1.4 facilitate users to copy and upload sequencing data to your S3 bucket in batch mode.

To copy files to/from the S3 bucket in AWS CLI, users can use the following command:

 aws s3 cp <source> <destination>

1) copy one sequencing file (sequencing_data.bam or equencing_data.cram) to the "data" directory located in my-s3-bucket

aws s3 cp sequencing_data.bam  s3://my-s3-bucket/data/aws s3 cp sequencing_data.cram s3://my-s3-bucket/data/

2) copy all files in my-data-dir into the "data" directory located in my-s3-bucket

aws s3 cp my-data-dir/ s3://my-s3-bucket/data/ --recursive