aws omics start-read-set-import-job

Imports a read set from the sequence store. AWS CLI reference

1 example 4 options Its page in the AWS CLI reference

Examples

from aws-cli, each command read by CmdID

To import a read set

The following start-read-set-import-job example imports a read set.

aws omics start-read-set-import-job --sequence-store-id 1234567890 --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ --sources file://readset-sources.json

Identify

--sequence-store-idThe read set's sequence store ID.

--role-arnA service role for the job.

--sourcesThe job's source files.

Contents of readset-sources.json:

[
    {
        "sourceFiles":
        {
            "source1": "s3://amzn-s3-demo-bucket/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam"
        },
        "sourceFileType": "BAM",
        "subjectId": "bam-subject",
        "sampleId": "bam-sample",
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
        "name": "HG00100"
    }
]

Its output

{
    "creationTime": "2022-11-23T01:36:38.158Z",
    "id": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

For more information, see Omics Storage in the Amazon Omics Developer Guide.

Options

4 in the AWS CLI reference

--client-tokenTo ensure that jobs don't run multiple times, specify a unique token for each job.

--role-arnA service role for the job.

--sequence-store-idThe read set's sequence store ID.

--sourcesThe job's source files.