Exporting HealthOmics read sets to an Amazon S3 bucket

You can export read sets as a batch export job to an Amazon S3 bucket. To do so, first create an IAM policy that has write access to the bucket, similar to the following IAM policy example.

{
"Version": "2012-10-17",
"Statement": [
  {
      "Effect": "Allow",
      "Action": [
          "s3:PutObject",
          "s3:GetBucketLocation"
       ],
       "Resource": [
          "arn:aws:s3:::amzn-s3-demo-bucket1",
          "arn:aws:s3:::amzn-s3-demo-bucket1/*"
       ]
  }
]
}                    

{
"Version": "2012-10-17",
"Statement": [
  {
      "Effect": "Allow",
      "Principal": {
          "Service": [
              "omics.amazonaws.com"
          ]
      },
      "Action": "sts:AssumeRole"
  }
]
}                  

After the IAM policy is in place, begin your read set export job. The following example shows you how to do this by using the start-read-set-export-job API operation. In the following example, replace all parameters, such as sequence store ID, destination , role ARN, and sources, with your input.

aws omics start-read-set-export-job 
--sequence-store-id sequence store id \
--destination valid s3 uri \
--role-arn role ARN \
--sources readSetId=read set id_1 readSetId=read set id_2                    

You receive the following response with information on the origin sequence store and the destination Amazon S3 bucket.

{
"id": <job-id>,
"sequenceStoreId": <sequence-store-id>,
"destination": <destination-s3-uri>,
"status": "SUBMITTED",
"creationTime": "2022-10-22T01:33:38.079000+00:00"
}                    

After the job starts, you can determine its status by using the get-read-set-export-job API operation, as shown in the following. Replace the sequence store ID and job ID with your sequence store ID and job ID, respectively.

aws omics get-read-set-export-job --id job-id --sequence-store-id sequence store ID

You can view all export jobs initialized for a sequence store by using the list-read-set-export-jobs API operation, as shown in the following. Replace the sequence store ID with your sequence store ID.

aws omics list-read-set-export-jobs --sequence-store-id sequence store ID.

{
"exportJobs": [
  {
      "id": <job-id>,
      "sequenceStoreId": <sequence-store-id>,
      "destination": <destination-s3-uri>,
      "status": "COMPLETED",
      "creationTime": "2022-10-22T01:33:38.079000+00:00",
      "completionTime": "2022-10-22T01:34:28.941000+00:00"
  }
]
}        

In addition to exporting your read sets, you can also share them by using the Amazon S3 access URIs. To learn more, see Accessing HealthOmics read sets with Amazon S3 URIs.