Exporting HealthOmics read sets to an Amazon S3 bucket - AWS HealthOmics

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.

JSON
{
  "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/*"
      ]
    }
  ]
}
JSON
{
"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.