HealthOmics examples using AWS CLI - AWS Command Line Interface
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HealthOmics examples using AWS CLI

The following code examples show you how to perform actions and implement common scenarios by using the AWS Command Line Interface with HealthOmics.

Actions are code excerpts from larger programs and must be run in context. While actions show you how to call individual service functions, you can see actions in context in their related scenarios.

Each example includes a link to the complete source code, where you can find instructions on how to set up and run the code in context.

Topics

Actions

The following code example shows how to use abort-multipart-read-set-upload.

AWS CLI

To stop a multipart read set upload

The following abort-multipart-read-set-upload example stops a multipart read set upload into your HealthOmics sequence store.

aws omics abort-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455

This command produces no output.

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

The following code example shows how to use accept-share.

AWS CLI

To accept a share of analytics store data

The following accept-share example accepts a share of HealthOmics analytics store data.

aws omics accept-share \
    ----share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

Output:

{
    "status": "ACTIVATING"
}

For more information, see Cross-account sharing in the AWS HealthOmics User Guide.

  • For API details, see AcceptShare in AWS CLI Command Reference.

The following code example shows how to use batch-delete-read-set.

AWS CLI

To delete multiple read sets

The following batch-delete-read-set example deletes two read sets.

aws omics batch-delete-read-set \
    --sequence-store-id 1234567890 \
    --ids 1234567890 0123456789

If there is an error deleting any of the specified read sets, the service returns an error list.

{
    "errors": [
        {
            "code": "",
            "id": "0123456789",
            "message": "The specified readset does not exist."
        }
    ]
}

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

The following code example shows how to use cancel-annotation-import-job.

AWS CLI

To cancel an annotation import job

The following cancel-annotation-import-job example cancels an annotation import job with ID 04f57618-xmpl-4fd0-9349-e5a85aefb997.

aws omics cancel-annotation-import-job \
    --job-id 04f57618-xmpl-4fd0-9349-e5a85aefb997

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

The following code example shows how to use cancel-run.

AWS CLI

To cancel a run

The following cancel-run example cancels a run with ID 1234567.

aws omics cancel-run \
    --id 1234567

For more information, see Run lifecycle in a workflow in the AWS HealthOmics User Guide.

  • For API details, see CancelRun in AWS CLI Command Reference.

The following code example shows how to use cancel-variant-import-job.

AWS CLI

To cancel a variant import job

The following cancel-variant-import-job example cancels a variant import job with ID 69cb65d6-xmpl-4a4a-9025-4565794b684e.

aws omics cancel-variant-import-job \
    --job-id 69cb65d6-xmpl-4a4a-9025-4565794b684e

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

The following code example shows how to use complete-multipart-read-set-upload.

AWS CLI

To conclude a multipart upload once you have uploaded all of the components.

The following complete-multipart-read-set-upload example concludes a multipart upload into a sequence store once all of the components have been uploaded.

aws omics complete-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --parts '[{"checksum":"gaCBQMe+rpCFZxLpoP6gydBoXaKKDA/Vobh5zBDb4W4=","partNumber":1,"partSource":"SOURCE1"}]'

Output:

{
    "readSetId": "0000000001"
    "readSetId": "0000000002"
    "readSetId": "0000000003"
}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

The following code example shows how to use create-annotation-store-version.

AWS CLI

To create a new version of an annotation store

The following create-annotation-store-version example creates a new version of an annotation store.

aws omics create-annotation-store-version \
    --name my_annotation_store \
    --version-name my_version

Output:

{
    "creationTime": "2023-07-21T17:15:49.251040+00:00",
    "id": "3b93cdef69d2",
    "name": "my_annotation_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:555555555555:referenceStore/6505293348/reference/5987565360"
    },
    "status": "CREATING",
    "versionName": "my_version"
}

For more information, see Creating new versions of annotation stores in the AWS HealthOmics User Guide.

The following code example shows how to use create-annotation-store.

AWS CLI

Example 1: To create a VCF annotation store

The following create-annotation-store example creates a VCF format annotation store.

aws omics create-annotation-store \
    --name my_ann_store \
    --store-format VCF \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890

Output:

{
    "creationTime": "2022-11-23T22:48:39.226492Z",
    "id": "0a91xmplc71f",
    "name": "my_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeFormat": "VCF"
}

Example 2: To create a TSV annotation store

The following create-annotation-store example creates a TSV format annotation store.

aws omics create-annotation-store \
    --name tsv_ann_store \
    --store-format TSV \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890 \
    --store-options file://tsv-store-options.json

tsv-store-options.json configures format options for annotations.

{
    "tsvStoreOptions": {
        "annotationType": "CHR_START_END_ZERO_BASE",
        "formatToHeader": {
            "CHR": "chromosome",
            "START": "start",
            "END": "end"
        },
        "schema": [
            {
                "chromosome": "STRING"
            },
            {
                "start": "LONG"
            },
            {
                "end": "LONG"
            },
            {
                "name": "STRING"
            }
        ]
    }
}

Output:

{
    "creationTime": "2022-11-30T01:28:08.525586Z",
    "id": "861cxmpl96b0",
    "name": "tsv_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeFormat": "TSV",
    "storeOptions": {
        "tsvStoreOptions": {
            "annotationType": "CHR_START_END_ZERO_BASE",
            "formatToHeader": {
                "CHR": "chromosome",
                "END": "end",
                "START": "start"
            },
            "schema": [
                {
                    "chromosome": "STRING"
                },
                {
                    "start": "LONG"
                },
                {
                    "end": "LONG"
                },
                {
                    "name": "STRING"
                }
            ]
        }
    }
}

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

The following code example shows how to use create-multipart-read-set-upload.

AWS CLI

To begin a multipart read set upload.

The following create-multipart-read-set-upload example initiates a multipart read set upload.

aws omics create-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --name HG00146 \
    --source-file-type FASTQ \
    --subject-id mySubject\
    --sample-id mySample\
    --description "FASTQ for HG00146"\
    --generated-from "1000 Genomes"

Output:

{
    "creationTime": "2022-07-13T23:25:20Z",
    "description": "FASTQ for HG00146",
    "generatedFrom": "1000 Genomes",
    "name": "HG00146",
    "sampleId": "mySample",
    "sequenceStoreId": "0123456789",
    "sourceFileType": "FASTQ",
    "subjectId": "mySubject",
    "uploadId": "1122334455"
}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

The following code example shows how to use create-reference-store.

AWS CLI

To create a reference store

The following create-reference-store example creates a reference store my-ref-store.

aws omics create-reference-store \
    --name my-ref-store

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
    "creationTime": "2022-11-22T22:13:25.947Z",
    "id": "1234567890",
    "name": "my-ref-store"
}

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

The following code example shows how to use create-run-group.

AWS CLI

To create a run group

The following create-run-group example creates a run group named cram-converter.

aws omics create-run-group \
    --name cram-converter \
    --max-cpus 20 \
    --max-gpus 10 \
    --max-duration 600 \
    --max-runs 5

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "id": "1234567",
    "tags": {}
}

For more information, see Creating run groups in the AWS HealthOmics User Guide.

The following code example shows how to use create-sequence-store.

AWS CLI

To create a sequence store

The following create-sequence-store example creates a sequence store.

aws omics create-sequence-store \
    --name my-seq-store

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890",
    "creationTime": "2022-11-23T01:24:33.629Z",
    "id": "1234567890",
    "name": "my-seq-store"
}

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

The following code example shows how to use create-share.

AWS CLI

To create a share of a HealthOmics analytics store

The following create-share example shows how to create a share of a HealthOmics analytics store that can be accepted by a subscriber outside the account.

aws omics create-share \
    --resource-arn "arn:aws:omics:us-west-2:555555555555:variantStore/omics_dev_var_store" \
    --principal-subscriber "123456789012" \
    --name "my_Share-123"

Output:

{
    "shareId": "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a",
    "name": "my_Share-123",
    "status": "PENDING"
}

For more information, see Cross-acount sharing in the AWS HealthOmics User Guide.

  • For API details, see CreateShare in AWS CLI Command Reference.

The following code example shows how to use create-variant-store.

AWS CLI

To create a variant store

The following create-variant-store example creates a variant store named my_var_store.

aws omics create-variant-store \
    --name my_var_store \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890

Output:

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING"
}

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

The following code example shows how to use create-workflow.

AWS CLI

To create a workflow

The following create-workflow example creates a WDL workflow.

aws omics create-workflow \
    --name cram-converter \
    --engine WDL \
    --definition-zip fileb://workflow-crambam.zip \
    --parameter-template file://workflow-params.json

workflow-crambam.zip is a ZIP archive containing a workflow definition. workflow-params.json defines runtime parameters for the workflow.

{
    "ref_fasta" : {
        "description": "Reference genome fasta file",
        "optional": false
    },
    "ref_fasta_index" : {
        "description": "Index of the reference genome fasta file",
        "optional": false
    },
    "ref_dict" : {
        "description": "dictionary file for 'ref_fasta'",
        "optional": false
    },
    "input_cram" : {
        "description": "The Cram file to convert to BAM",
        "optional": false
    },
    "sample_name" : {
        "description": "The name of the input sample, used to name the output BAM",
        "optional": false
    }
}

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
    "id": "1234567",
    "status": "CREATING",
    "tags": {}
}

For more information, see Creating private workflows in the AWS HealthOmics User Guide.

The following code example shows how to use delete-annotation-store-versions.

AWS CLI

To delete an annotation store version

The following delete-annotation-store-versions example deletes an annotation store version.

aws omics delete-annotation-store-versions \
    --name my_annotation_store \
    --versions my_version

Output:

{
    "errors": []
}

For more information, see Creating new versions of annotation stores in the AWS HealthOmics User Guide.

The following code example shows how to use delete-annotation-store.

AWS CLI

To delete an annotation store

The following delete-annotation-store example deletes an annotation store named my_vcf_store.

aws omics delete-annotation-store \
    --name my_vcf_store

Output:

{
    "status": "DELETING"
}

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

The following code example shows how to use delete-reference-store.

AWS CLI

To delete a reference store

The following delete-reference-store example deletes a reference store with ID 1234567890.

aws omics delete-reference-store \
    --id 1234567890

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

The following code example shows how to use delete-reference.

AWS CLI

To delete a reference

The following delete-reference example deletes a reference.

aws omics delete-reference \
    --reference-store-id 1234567890 \
    --id 1234567890

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

The following code example shows how to use delete-run-group.

AWS CLI

To delete a run group

The following delete-run-group example deletes a run group with ID 1234567.

aws omics delete-run-group \
    --id 1234567

For more information, see Deleting runs and run groups in the AWS HealthOmics User Guide.

The following code example shows how to use delete-run.

AWS CLI

To delete a workflow run

The following delete-run example deletes a run with ID 1234567.

aws omics delete-run \
    --id 1234567

For more information, see Deleting runs and run groups in the AWS HealthOmics User Guide.

  • For API details, see DeleteRun in AWS CLI Command Reference.

The following code example shows how to use delete-sequence-store.

AWS CLI

To delete a sequence store

The following delete-sequence-store example deletes a sequence store with ID 1234567890.

aws omics delete-sequence-store \
    --id 1234567890

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

The following code example shows how to use delete-share.

AWS CLI

To delete a share of HealthOmics analytics data

The following delete-share example deletes a cross-account share of analytics data.

aws omics delete-share \
    --share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

Output:

{
    "status": "DELETING"
}

For more information, see Cross-account sharing in the AWS HealthOmics User Guide.

  • For API details, see DeleteShare in AWS CLI Command Reference.

The following code example shows how to use delete-variant-store.

AWS CLI

To delete a variant store

The following delete-variant-store example deletes a variant store named my_var_store.

aws omics delete-variant-store \
    --name my_var_store

Output:

{
    "status": "DELETING"
}

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

The following code example shows how to use delete-workflow.

AWS CLI

To delete a workflow

The following delete-workflow example deletes a workflow with ID 1234567.

aws omics delete-workflow \
    --id 1234567

For more information, see Delete a private workflow in the AWS HealthOmics User Guide.

The following code example shows how to use get-annotation-import-job.

AWS CLI

To view an annotation import job

The following get-annotation-import-job example gets details about an annotation import job.

aws omics get-annotation-import-job \
    --job-id 984162c7-xmpl-4d23-ab47-286f7950bfbf

Output:

{
    "creationTime": "2022-11-30T01:40:11.017746Z",
    "destinationName": "tsv_ann_store",
    "id": "984162c7-xmpl-4d23-ab47-286f7950bfbf",
    "items": [
        {
            "jobStatus": "COMPLETED",
            "source": "s3://omics-artifacts-01d6xmpl4e72dd32/targetedregions.bed.gz"
        }
    ],
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "runLeftNormalization": false,
    "status": "COMPLETED",
    "updateTime": "2022-11-30T01:42:39.134009Z"
}

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

The following code example shows how to use get-annotation-store-version.

AWS CLI

To retrieve the metadata for an annotation store version

The following get-annotation-store-version example retrieves the metadata for the requested annotation store version.

aws omics get-annotation-store-version \
    --name my_annotation_store \
    --version-name my_version

Output:

{
    "storeId": "4934045d1c6d",
    "id": "2a3f4a44aa7b",
    "status": "ACTIVE",
    "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version",
    "name": "my_annotation_store",
    "versionName": "my_version",
    "creationTime": "2023-07-21T17:15:49.251040+00:00",
    "updateTime": "2023-07-21T17:15:56.434223+00:00",
    "statusMessage": "",
    "versionSizeBytes": 0
}

For more information, see Creating new versions of annotation stores in the AWS HealthOmics User Guide.

The following code example shows how to use get-annotation-store.

AWS CLI

To view an annotation store

The following get-annotation-store example gets details about an annotation store named my_ann_store.

aws omics get-annotation-store \
    --name my_ann_store

Output:

{
    "creationTime": "2022-11-23T22:48:39.226492Z",
    "id": "0a91xmplc71f",
    "name": "my_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeArn": "arn:aws:omics:us-west-2:123456789012:annotationStore/my_ann_store",
    "storeFormat": "VCF",
    "storeSizeBytes": 0,
    "tags": {}
}

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

The following code example shows how to use get-read-set-activation-job.

AWS CLI

To view a read set activation job

The following get-read-set-activation-job example gets details about a read set activation job.

aws omics get-read-set-activation-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

Output:

{
    "completionTime": "2022-12-06T22:33:42.828Z",
    "creationTime": "2022-12-06T22:32:45.213Z",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "sources": [
        {
            "readSetId": "1234567890",
            "status": "FINISHED",
            "statusMessage": "No activation needed as read set is already in ACTIVATING or ACTIVE state."
        }
    ],
    "status": "COMPLETED",
    "statusMessage": "The job completed successfully."
}

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

The following code example shows how to use get-read-set-export-job.

AWS CLI

To view a read set export job

The following get-read-set-export-job example gets details about a read set export job.

aws omics get-read-set-export-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

Output:

{
    "completionTime": "2022-12-06T22:39:14.491Z",
    "creationTime": "2022-12-06T22:37:18.612Z",
    "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "COMPLETED",
    "statusMessage": "The job is submitted and will start soon."
}

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

The following code example shows how to use get-read-set-import-job.

AWS CLI

To view a read set import job

The following get-read-set-import-job example gets details about a read set import job.

aws omics get-read-set-import-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

Output:

{
    "creationTime": "2022-11-23T01:36:38.158Z",
    "id": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sequenceStoreId": "1234567890",
    "sources": [
        {
            "name": "HG00100",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "bam-sample",
            "sourceFileType": "BAM",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam",
                "source2": ""
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "bam-subject",
            "tags": {
                "aws:omics:sampleId": "bam-sample",
                "aws:omics:subjectId": "bam-subject"
            }
        },
        {
            "name": "HG00146",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "fastq-sample",
            "sourceFileType": "FASTQ",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/SRR233106_1.filt.fastq.gz",
                "source2": "s3://omics-artifacts-01d6xmpl4e72dd32/SRR233106_2.filt.fastq.gz"
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "fastq-subject",
            "tags": {
                "aws:omics:sampleId": "fastq-sample",
                "aws:omics:subjectId": "fastq-subject"
            }
        },
        {
            "name": "HG00096",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "cram-sample",
            "sourceFileType": "CRAM",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram",
                "source2": ""
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "cram-subject",
            "tags": {
                "aws:omics:sampleId": "cram-sample",
                "aws:omics:subjectId": "cram-subject"
            }
        }
    ],
    "status": "IN_PROGRESS",
    "statusMessage": "The job is currently in progress."
}

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

The following code example shows how to use get-read-set-metadata.

AWS CLI

To view a read set

The following get-read-set-metadata example gets details about a read set's files.

aws omics get-read-set-metadata \
    --sequence-store-id 1234567890 \
    --id 1234567890

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890/readSet/1234567890",
    "creationTime": "2022-11-23T21:55:00.515Z",
    "fileType": "FASTQ",
    "files": {
        "source1": {
            "contentLength": 310054739,
            "partSize": 104857600,
            "totalParts": 3
        },
        "source2": {
            "contentLength": 307846621,
            "partSize": 104857600,
            "totalParts": 3
        }
    },
    "id": "1234567890",
    "name": "HG00146",
    "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
    "sampleId": "fastq-sample",
    "sequenceInformation": {
        "alignment": "UNALIGNED",
        "totalBaseCount": 677717384,
        "totalReadCount": 8917334
    },
    "sequenceStoreId": "1234567890",
    "status": "ACTIVE",
    "subjectId": "fastq-subject"
}

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

The following code example shows how to use get-read-set.

AWS CLI

To download a read set

The following get-read-set example downloads part 3 of a read set as 1234567890.3.bam.

aws omics get-read-set \
    --sequence-store-id 1234567890 \
    --id 1234567890 \
    --part-number 3  1234567890.3.bam

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

  • For API details, see GetReadSet in AWS CLI Command Reference.

The following code example shows how to use get-reference-import-job.

AWS CLI

To view a reference import job

The following get-reference-import-job example example gets details about a reference import job.

aws omics get-reference-import-job \
    --reference-store-id 1234567890 \
    --id 1234567890

Output:

{
    "creationTime": "2022-11-22T22:25:41.124Z",
    "id": "1234567890",
    "referenceStoreId": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sources": [
        {
            "name": "assembly-38",
            "sourceFile": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress."
        }
    ],
    "status": "IN_PROGRESS",
    "statusMessage": "The job is currently in progress."
}

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

The following code example shows how to use get-reference-metadata.

AWS CLI

To view a reference

The following get-reference-metadata example gets details about a reference.

aws omics get-reference-metadata \
    --reference-store-id 1234567890 \
    --id 1234567890

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
    "creationTime": "2022-11-22T22:27:09.033Z",
    "files": {
        "index": {
            "contentLength": 160928,
            "partSize": 104857600,
            "totalParts": 1
        },
        "source": {
            "contentLength": 3249912778,
            "partSize": 104857600,
            "totalParts": 31
        }
    },
    "id": "1234567890",
    "md5": "7ff134953dcca8c8997453bbb80b6b5e",
    "name": "assembly-38",
    "referenceStoreId": "1234567890",
    "status": "ACTIVE",
    "updateTime": "2022-11-22T22:27:09.033Z"
}

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

The following code example shows how to use get-reference-store.

AWS CLI

To view a reference store

The following get-reference-store example gets details about a reference store.

aws omics get-reference-store \
    --id 1234567890

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
    "creationTime": "2022-09-23T23:27:20.364Z",
    "id": "1234567890",
    "name": "my-rstore-0"
}

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

The following code example shows how to use get-reference.

AWS CLI

To download a genome reference

The following get-reference example downloads part 1 of a genome as hg38.1.fa.

aws omics get-reference \
    --reference-store-id 1234567890 \
    --id 1234567890 \
    --part-number 1 hg38.1.fa

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

  • For API details, see GetReference in AWS CLI Command Reference.

The following code example shows how to use get-run-group.

AWS CLI

To view a run group

The following get-run-group example gets details about a run group.

aws omics get-run-group \
    --id 1234567

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "creationTime": "2022-12-01T00:58:42.915219Z",
    "id": "1234567",
    "maxCpus": 20,
    "maxDuration": 600,
    "name": "cram-convert",
    "tags": {}
}

For more information, see Creating run groups in the AWS HealthOmics User Guide.

  • For API details, see GetRunGroup in AWS CLI Command Reference.

The following code example shows how to use get-run-task.

AWS CLI

To view a task

The following get-run-task example gets details about a workflow task.

aws omics get-run-task \
    --id 1234567 \
    --task-id 1234567

Output:

{
    "cpus": 1,
    "creationTime": "2022-11-30T23:13:00.718651Z",
    "logStream": "arn:aws:logs:us-west-2:123456789012:log-group:/aws/omics/WorkflowLog:log-stream:run/1234567/task/1234567",
    "memory": 15,
    "name": "CramToBamTask",
    "startTime": "2022-11-30T23:17:47.016Z",
    "status": "COMPLETED",
    "stopTime": "2022-11-30T23:18:21.503Z",
    "taskId": "1234567"
}

For more information, see Task lifecycle in a HealthOmics run in the AWS HealthOmics User Guide.

  • For API details, see GetRunTask in AWS CLI Command Reference.

The following code example shows how to use get-run.

AWS CLI

To view a workflow run

The following get-run example gets details about a workflow run.

aws omics get-run \
    --id 1234567

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
    "creationTime": "2022-11-30T22:58:22.615865Z",
    "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
    "id": "1234567",
    "name": "cram-to-bam",
    "outputUri": "s3://omics-artifacts-01d6xmpl4e72dd32/workflow-output/",
    "parameters": {
        "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
        "ref_fasta_index": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai",
        "ref_fasta": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
        "sample_name": "NA12878",
        "input_cram": "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram"
    },
    "resourceDigests": {
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai": "etag:f76371b113734a56cde236bc0372de0a",
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict": "etag:3884c62eb0e53fa92459ed9bff133ae6",
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta": "etag:e307d81c605fb91b7720a08f00276842-388",
        "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram": "etag:a9f52976381286c6143b5cc681671ec6"
    },
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "startedBy": "arn:aws:iam::123456789012:user/laptop-2020",
    "status": "STARTING",
    "tags": {},
    "workflowId": "1234567",
    "workflowType": "PRIVATE"
}

For more information, see Run lifecycle in a workflow in the AWS HealthOmics User Guide.

  • For API details, see GetRun in AWS CLI Command Reference.

The following code example shows how to use get-sequence-store.

AWS CLI

To view a sequence store

The following get-sequence-store example gets details about a sequence store with ID 1234567890.

aws omics get-sequence-store \
    --id 1234567890

Output:

{
    "arn": "arn:aws:omics:us-east-1:123456789012:sequenceStore/1234567890",
    "creationTime": "2022-11-23T19:55:48.376Z",
    "id": "1234567890",
    "name": "my-seq-store"
}

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

The following code example shows how to use get-share.

AWS CLI

To retrieves the metadata about a share of a HealthOmics analytics data

The following get-share example retrieves the metadata for a cross-account share of analytics data.

aws omics get-share \
    --share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

Output:

{
    "share": {
        "shareId": "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a",
        "name": "my_Share-123",
        "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/omics_dev_var_store",
        "principalSubscriber": "123456789012",
        "ownerId": "555555555555",
        "status": "PENDING"
    }
}

For more information, see Cross-account sharing in the AWS HealthOmics User Guide.

  • For API details, see GetShare in AWS CLI Command Reference.

The following code example shows how to use get-variant-import-job.

AWS CLI

To view a variant import job

The following get-variant-import-job example gets details about a variant import job.

aws omics get-variant-import-job \
    --job-id edd7b8ce-xmpl-47e2-bc99-258cac95a508

Output:

{
    "creationTime": "2022-11-23T22:42:50.037812Z",
    "destinationName": "my_var_store",
    "id": "edd7b8ce-xmpl-47e2-bc99-258cac95a508",
    "items": [
        {
            "jobStatus": "IN_PROGRESS",
            "source": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.known_indels.vcf.gz"
        }
    ],
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "runLeftNormalization": false,
    "status": "IN_PROGRESS",
    "updateTime": "2022-11-23T22:43:05.898309Z"
}

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

The following code example shows how to use get-variant-store.

AWS CLI

To view a variant store

The following get-variant-store example gets details about a variant store.

aws omics get-variant-store \
    --name my_var_store

Output:

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/my_var_store",
    "storeSizeBytes": 0,
    "tags": {},
    "updateTime": "2022-11-23T22:09:24.931711Z"
}

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

The following code example shows how to use get-workflow.

AWS CLI

To view a workflow

The following get-workflow example gets details about a workflow with ID 1234567.

aws omics get-workflow \
    --id 1234567

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
    "creationTime": "2022-11-30T22:33:16.225368Z",
    "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
    "engine": "WDL",
    "id": "1234567",
    "main": "workflow-crambam.wdl",
    "name": "cram-converter",
    "parameterTemplate": {
        "ref_dict": {
            "description": "dictionary file for 'ref_fasta'"
        },
        "ref_fasta_index": {
            "description": "Index of the reference genome fasta file"
        },
        "ref_fasta": {
            "description": "Reference genome fasta file"
        },
        "input_cram": {
            "description": "The Cram file to convert to BAM"
        },
        "sample_name": {
            "description": "The name of the input sample, used to name the output BAM"
        }
    },
    "status": "ACTIVE",
    "statusMessage": "workflow-crambam.wdl\n    workflow CramToBamFlow\n        call CramToBamTask\n        call ValidateSamFile\n    task CramToBamTask\n    task ValidateSamFile\n",
    "tags": {},
    "type": "PRIVATE"
}

For more information, see Creating private workflows in the AWS HealthOmics User Guide.

  • For API details, see GetWorkflow in AWS CLI Command Reference.

The following code example shows how to use list-annotation-import-jobs.

AWS CLI

To get a list of annotation import jobs

The following list-annotation-import-jobs gets a list of annotation import jobs.

aws omics list-annotation-import-jobs

Output:

{
    "annotationImportJobs": [
        {
            "creationTime": "2022-11-30T01:39:41.478294Z",
            "destinationName": "gff_ann_store",
            "id": "18a9e792-xmpl-4869-a105-e5b602900444",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-30T01:47:09.145178Z"
        },
        {
            "creationTime": "2022-11-30T00:45:58.007838Z",
            "destinationName": "my_ann_store",
            "id": "4e9eafc8-xmpl-431e-a0b2-3bda27cb600a",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "FAILED",
            "updateTime": "2022-11-30T00:47:01.706325Z"
        }
    ]
}

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

The following code example shows how to use list-annotation-store-versions.

AWS CLI

To list all the versions of an annotation store.

The following list-annotation-store-versions example lists all versions that exist of an annotation store.

aws omics list-annotation-store-versions \
    --name my_annotation_store

Output:

{
    "annotationStoreVersions": [
        {
        "storeId": "4934045d1c6d",
        "id": "2a3f4a44aa7b",
        "status": "CREATING",
        "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version_2",
        "name": "my_annotation_store",
        "versionName": "my_version_2",
        "creation Time": "2023-07-21T17:20:59.380043+00:00",
        "versionSizeBytes": 0
},
{
     "storeId": "4934045d1c6d",
     "id": "4934045d1c6d",
     "status": "ACTIVE",
     "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version_1",
     "name": "my_annotation_store",
     "versionName": "my_version_1",
     "creationTime": "2023-07-21T17:15:49.251040+00:00",
     "updateTime": "2023-07-21T17:15:56.434223+00:00",
     "statusMessage": "",
     "versionSizeBytes": 0
     }

}

For more information, see Creating new versions of annotation stores in the AWS HealthOmics User Guide.

The following code example shows how to use list-annotation-stores.

AWS CLI

To get a list of annotation stores

The following list-annotation-stores example gets a list of annotation stores.

aws omics list-annotation-stores

Output:

{
    "annotationStores": [
        {
            "creationTime": "2022-11-23T22:48:39.226492Z",
            "id": "0a91xmplc71f",
            "name": "my_ann_store",
            "reference": {
                "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
            },
            "status": "ACTIVE",
            "statusMessage": "",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:annotationStore/my_ann_store",
            "storeFormat": "VCF",
            "storeSizeBytes": 0,
            "updateTime": "2022-11-23T22:53:27.372840Z"
        }
    ]
}

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

The following code example shows how to use list-multipart-read-set-uploads.

AWS CLI

To list all multipart read set uploads and their statuses.

The following list-multipart-read-set-uploads example lists all multipart read set uploads and their statuses.

aws omics list-multipart-read-set-uploads \
    --sequence-store-id 0123456789

Output:

{
"uploads":
    [
        {
           "sequenceStoreId": "0123456789",
           "uploadId": "8749584421",
           "sourceFileType": "FASTQ",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "name": "HG00146",
            "description": "FASTQ for HG00146",
            "creationTime": "2023-11-29T19:22:51.349298+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "5290538638",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00146",
            "description": "BAM for HG00146",
            "creationTime": "2023-11-29T19:23:33.116516+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "4174220862",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00147",
            "description": "BAM for HG00147",
            "creationTime": "2023-11-29T19:23:47.007866+00:00"
        }
    ]
}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

The following code example shows how to use list-read-set-activation-jobs.

AWS CLI

To get a list of read set activation jobs

The following list-read-set-activation-jobs example gets a list of activation jobs for a sequence store with id 1234567890.

aws omics list-read-set-activation-jobs \
    --sequence-store-id 1234567890

Output:

{
    "activationJobs": [
        {
            "completionTime": "2022-12-06T22:33:42.828Z",
            "creationTime": "2022-12-06T22:32:45.213Z",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-12-06T22:35:10.100Z",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "IN_PROGRESS"
        }
    ]
}

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

The following code example shows how to use list-read-set-export-jobs.

AWS CLI

To gets a list of read set export jobs

The following list-read-set-export-jobs example gets a list of export jobs for a sequence store with id 1234567890.

aws omics list-read-set-export-jobs \
    --sequence-store-id 1234567890

Output:

{
    "exportJobs": [
        {
            "completionTime": "2022-12-06T22:39:14.491Z",
            "creationTime": "2022-12-06T22:37:18.612Z",
            "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-12-06T22:38:04.871Z",
            "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "IN_PROGRESS"
        }
    ]
}

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

The following code example shows how to use list-read-set-import-jobs.

AWS CLI

To get a list of read set import jobs

The following list-read-set-import-jobs example gets a list of import jobs for a sequence store with id 1234567890.

aws omics list-read-set-import-jobs \
    --sequence-store-id 1234567890

Output:

{
    "importJobs": [
        {
            "completionTime": "2022-11-29T18:17:49.244Z",
            "creationTime": "2022-11-29T17:32:47.700Z",
            "id": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "completionTime": "2022-11-23T22:01:34.090Z",
            "creationTime": "2022-11-23T21:52:43.289Z",
            "id": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED_WITH_FAILURES"
        }
    ]
}

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

The following code example shows how to use list-read-set-upload-parts.

AWS CLI

To list all parts in a requested multipart upload for a sequence store.

The following list-read-set-upload-parts example list all parts in a requested multipart upload for a sequence store.

aws omics list-read-set-upload-parts \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --part-source SOURCE1

Output:

{
    "parts": [
        {
            "partNumber": 1,
            "partSize": 94371840,
            "file": "SOURCE1",
            "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635",
            "lastUpdatedTime": "2023-02-02T20:14:47.533000+00:00"
        }
        {
            "partNumber": 2,
            "partSize": 10471840,
            "file": "SOURCE1",
            "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635",
            "lastUpdatedTime": "2023-02-02T20:14:47.533000+00:00"
        }
      ]

}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.

The following code example shows how to use list-read-sets.

AWS CLI

To get a list of read sets

The following list-read-sets example gets a list of read sets for a sequence store with id 1234567890.

aws omics list-read-sets \
    --sequence-store-id 1234567890

Output:

{
    "readSets": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890/readSet/1234567890",
            "creationTime": "2022-11-23T21:55:00.515Z",
            "fileType": "FASTQ",
            "id": "1234567890",
            "name": "HG00146",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "fastq-sample",
            "sequenceStoreId": "1234567890",
            "status": "ACTIVE",
            "subjectId": "fastq-subject"
        }
    ]
}

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

  • For API details, see ListReadSets in AWS CLI Command Reference.

The following code example shows how to use list-reference-import-jobs.

AWS CLI

To get a list of reference import jobs

The following list-reference-import-jobs example gets a list of reference import jobs for a reference store with id 1234567890.

aws omics list-reference-import-jobs \
    --reference-store-id 1234567890

Output:

{
    "importJobs": [
        {
            "completionTime": "2022-11-23T19:54:58.204Z",
            "creationTime": "2022-11-23T19:53:20.729Z",
            "id": "1234567890",
            "referenceStoreId": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-11-23T20:34:03.250Z",
            "id": "1234567890",
            "referenceStoreId": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "status": "IN_PROGRESS"
        }
    ]
}

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

The following code example shows how to use list-reference-stores.

AWS CLI

To get a list of reference stores

The following list-reference-stores example gets a list of reference stores.

aws omics list-reference-stores

Output:

{
    "referenceStores": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
            "creationTime": "2022-11-22T22:13:25.947Z",
            "id": "1234567890",
            "name": "my-ref-store"
        }
    ]
}

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

The following code example shows how to use list-references.

AWS CLI

To get a list of references

The following list-references example gets a list of genome references for a reference store with id 1234567890.

aws omics list-references \
    --reference-store-id 1234567890

Output:

{
    "references": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "creationTime": "2022-11-22T22:27:09.033Z",
            "id": "1234567890",
            "md5": "7ff134953dcca8c8997453bbb80b6b5e",
            "name": "assembly-38",
            "referenceStoreId": "1234567890",
            "status": "ACTIVE",
            "updateTime": "2022-11-22T22:27:09.033Z"
        }
    ]
}

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

The following code example shows how to use list-run-groups.

AWS CLI

To get a list of run groups

The following list-run-groups example gets a list of run groups.

aws omics list-run-groups

Output:

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
            "creationTime": "2022-12-01T00:58:42.915219Z",
            "id": "1234567",
            "maxCpus": 20,
            "maxDuration": 600,
            "name": "cram-convert"
        }
    ]
}

For more information, see Creating run groups in the AWS HealthOmics User Guide.

  • For API details, see ListRunGroups in AWS CLI Command Reference.

The following code example shows how to use list-run-tasks.

AWS CLI

To get a list of tasks

The following list-run-tasks example gets a list of tasks for a workflow run.

aws omics list-run-tasks \
    --id 1234567

Output:

{
    "items": [
        {
            "cpus": 1,
            "creationTime": "2022-11-30T23:13:00.718651Z",
            "memory": 15,
            "name": "CramToBamTask",
            "startTime": "2022-11-30T23:17:47.016Z",
            "status": "COMPLETED",
            "stopTime": "2022-11-30T23:18:21.503Z",
            "taskId": "1234567"
        },
        {
            "cpus": 1,
            "creationTime": "2022-11-30T23:18:32.315606Z",
            "memory": 4,
            "name": "ValidateSamFile",
            "startTime": "2022-11-30T23:23:40.165Z",
            "status": "COMPLETED",
            "stopTime": "2022-11-30T23:24:14.766Z",
            "taskId": "1234567"
        }
    ]
}

For more information, see Task lifecycle in a HealthOmics run in the AWS HealthOmics User Guide.

  • For API details, see ListRunTasks in AWS CLI Command Reference.

The following code example shows how to use list-runs.

AWS CLI

To get a list of workflow runs

The following list-runs example gets a list of workflow runs.

aws omics list-runs

Output:

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-02T23:20:01.202074Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "priority": 1,
            "startTime": "2022-12-02T23:29:18.115Z",
            "status": "COMPLETED",
            "stopTime": "2022-12-02T23:57:54.428812Z",
            "storageCapacity": 10,
            "workflowId": "1234567"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-03T00:16:57.180066Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "priority": 1,
            "startTime": "2022-12-03T00:26:50.233Z",
            "status": "FAILED",
            "stopTime": "2022-12-03T00:37:21.451340Z",
            "storageCapacity": 10,
            "workflowId": "1234567"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-05T17:57:08.444817Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "status": "STARTING",
            "workflowId": "1234567"
        }
    ]
}

For more information, see Run lifecycle in a workflow in the AWS HealthOmics User Guide.

  • For API details, see ListRuns in AWS CLI Command Reference.

The following code example shows how to use list-sequence-stores.

AWS CLI

To get a list of sequence stores

The following list-sequence-stores example gets a list of sequence stores.

aws omics list-sequence-stores

Output:

{
    "sequenceStores": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890",
            "creationTime": "2022-11-23T01:24:33.629Z",
            "id": "1234567890",
            "name": "my-seq-store"
        }
    ]
}

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

The following code example shows how to use list-shares.

AWS CLI

To list the available shares of a HealthOmics analytics data

The following list-shares example lists all shares that have been created for a resource-owner.

aws omics list-shares \
    --resource-owner SELF

Output:

{
    "shares": [
        {
            "shareId": "595c1cbd-a008-4eca-a887-954d30c91c6e",
            "name": "myShare",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_1",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "PENDING"
        }
        {
            "shareId": "39b65d0d-4368-4a19-9814-b0e31d73c10a",
            "name": "myShare3456",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_2",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "ACTIVE"
        },
        {
            "shareId": "203152f5-eef9-459d-a4e0-a691668d44ef",
            "name": "myShare4",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_3",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "ACTIVE"
        }
    ]
}

For more information, see Cross-account sharing in the AWS HealthOmics User Guide.

  • For API details, see ListShares in AWS CLI Command Reference.

The following code example shows how to use list-tags-for-resource.

AWS CLI

To get a list of tags

The following list-tags-for-resource example gets a list of tags for a workflow with id 1234567.

aws omics list-tags-for-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567

Output:

{
    "tags": {
        "department": "analytics"
    }
}

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

The following code example shows how to use list-variant-import-jobs.

AWS CLI

To get a list of variant import jobs

The following list-variant-import-jobs example gets a list of variant import jobs.

aws omics list-variant-import-jobs

Output:

{
    "variantImportJobs": [
        {
            "creationTime": "2022-11-23T22:47:02.514002Z",
            "destinationName": "my_var_store",
            "id": "69cb65d6-xmpl-4a4a-9025-4565794b684e",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-23T22:49:17.976597Z"
        },
        {
            "creationTime": "2022-11-23T22:42:50.037812Z",
            "destinationName": "my_var_store",
            "id": "edd7b8ce-xmpl-47e2-bc99-258cac95a508",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-23T22:45:26.009880Z"
        }
    ]
}

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

The following code example shows how to use list-variant-stores.

AWS CLI

To get a list of variant stores

The following list-variant-stores example gets a list of variant stores.

aws omics list-variant-stores

Output:

{
    "variantStores": [
        {
            "creationTime": "2022-11-23T22:09:07.534499Z",
            "id": "02dexmplcfdd",
            "name": "my_var_store",
            "reference": {
                "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
            },
            "status": "CREATING",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/my_var_store",
            "storeSizeBytes": 0,
            "updateTime": "2022-11-23T22:09:24.931711Z"
        },
        {
            "creationTime": "2022-09-23T23:00:09.140265Z",
            "id": "8777xmpl1a24",
            "name": "myvstore0",
            "status": "ACTIVE",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/myvstore0",
            "storeSizeBytes": 0,
            "updateTime": "2022-09-23T23:03:26.013220Z"
        }
    ]
}

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

The following code example shows how to use list-workflows.

AWS CLI

To get a list of workflows

The following list-workflows example gets a list of workflows.

aws omics list-workflows

Output:

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
            "creationTime": "2022-09-23T23:08:22.041227Z",
            "digest": "nSCNo/qMWFxmplXpUdokXJnwgneOaxyyc2YOxVxrJTE=",
            "id": "1234567",
            "name": "my-wkflow-0",
            "status": "ACTIVE",
            "type": "PRIVATE"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
            "creationTime": "2022-11-30T22:33:16.225368Z",
            "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
            "id": "1234567",
            "name": "cram-converter",
            "status": "ACTIVE",
            "type": "PRIVATE"
        }
    ]
}

For more information, see Creating private workflows in the AWS HealthOmics User Guide.

  • For API details, see ListWorkflows in AWS CLI Command Reference.

The following code example shows how to use start-annotation-import-job.

AWS CLI

To import annotations

The following start-annotation-import-job example imports annotations from Amazon S3.

aws omics start-annotation-import-job \
    --destination-name tsv_ann_store \
    --no-run-left-normalization \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --items source=s3://omics-artifacts-01d6xmpl4e72dd32/targetedregions.bed.gz

Output:

{
    "jobId": "984162c7-xmpl-4d23-ab47-286f7950bfbf"
}

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

The following code example shows how to use start-read-set-activation-job.

AWS CLI

To activate an archived read set

The following start-read-set-activation-job example activates two read sets.

aws omics start-read-set-activation-job \
    --sequence-store-id 1234567890 \
    --sources readSetId=1234567890 readSetId=1234567890

Output:

{
    "creationTime": "2022-12-06T22:35:10.100Z",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

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

The following code example shows how to use start-read-set-export-job.

AWS CLI

To export a read set

The following start-read-set-export-job example exports two read sets to Amazon S3.

   aws omics start-read-set-export-job \
       --sequence-store-id 1234567890 \
       --sources readSetId=1234567890 readSetId=1234567890 \
       --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ
\
       --destination s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/

Output:

{
    "creationTime": "2022-12-06T22:37:18.612Z",
    "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

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

The following code example shows how to use start-read-set-import-job.

AWS CLI

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

readset-sources.json is a JSON document with the following content.

[
    {
        "sourceFiles":
        {
            "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/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"
    }
]

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.

The following code example shows how to use start-reference-import-job.

AWS CLI

To import a reference genome

The following start-reference-import-job example imports a reference genome from Amazon S3.

aws omics start-reference-import-job \
    --reference-store-id 1234567890 \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --sources sourceFile=s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta,name=assembly-38

Output:

{
    "creationTime": "2022-11-22T22:25:41.124Z",
    "id": "1234567890",
    "referenceStoreId": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "status": "SUBMITTED"
}

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

The following code example shows how to use start-run.

AWS CLI

To run a workflow

The following start-run example runs a workflow with ID 1234567.

aws omics start-run \
    --workflow-id 1234567 \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --name 'cram-to-bam' \
    --output-uri s3://omics-artifacts-01d6xmpl4e72dd32/workflow-output/ \
    --run-group-id 1234567 \
    --priority 1 \
    --storage-capacity 10 \
    --log-level ALL \
    --parameters file://workflow-inputs.json

workflow-inputs.json is a JSON document with the following content.

{
    "sample_name": "NA12878",
    "input_cram": "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram",
    "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
    "ref_fasta": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
    "ref_fasta_index": "omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai"
}

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
    "id": "1234567",
    "status": "PENDING",
    "tags": {}
}

For more information, see Starting a run in the AWS HealthOmics User Guide.

To load source files from Amazon Omics

You can also load source files from Amazon Omics storage, by using service-specific URIs. The following example workflow-inputs.json file uses Amazon Omics URIs for read set and reference genome sources.

{
    "sample_name": "NA12878",
    "input_cram": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/readSet/1234567890/source1",
    "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
    "ref_fasta": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/reference/1234567890",
    "ref_fasta_index": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/reference/1234567890/index"
}

  • For API details, see StartRun in AWS CLI Command Reference.

The following code example shows how to use start-variant-import-job.

AWS CLI

To import a variant file

The following start-variant-import-job example imports a VCF format variant file.

aws omics start-variant-import-job \
    --destination-name my_var_store \
    --no-run-left-normalization  \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --items source=s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.known_indels.vcf.gz

Output:

{
    "jobId": "edd7b8ce-xmpl-47e2-bc99-258cac95a508"
}

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

The following code example shows how to use tag-resource.

AWS CLI

To tag a resource

The following tag-resource example adds a department tag to a workflow with id 1234567.

aws omics tag-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \
    --tags department=analytics

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

  • For API details, see TagResource in AWS CLI Command Reference.

The following code example shows how to use untag-resource.

AWS CLI

To remove a tag from a resource

The following untag-resource example removes the department tag from a workflow.

aws omics untag-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \
    --tag-keys department

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

  • For API details, see UntagResource in AWS CLI Command Reference.

The following code example shows how to use update-annotation-store.

AWS CLI

To update an annotation store

The following update-annotation-store example updates the description of an annotation store named my_vcf_store.

aws omics update-annotation-store \
    --name my_vcf_store \
    --description "VCF annotation store"

Output:

{
    "creationTime": "2022-12-05T18:00:56.101860Z",
    "description": "VCF annotation store",
    "id": "bd6axmpl2444",
    "name": "my_vcf_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "ACTIVE",
    "storeFormat": "VCF",
    "updateTime": "2022-12-05T18:13:16.100051Z"
}

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

The following code example shows how to use update-run-group.

AWS CLI

To update a run group

The following update-run-group example updates the settings of a run group with id 1234567.

aws omics update-run-group \
    --id 1234567 \
    --max-cpus 10

Output:

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "creationTime": "2022-12-01T00:58:42.915219Z",
    "id": "1234567",
    "maxCpus": 10,
    "maxDuration": 600,
    "name": "cram-convert",
    "tags": {}
}

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

The following code example shows how to use update-variant-store.

AWS CLI

To update a variant store

The following update-variant-store example updates the description of a variant store named my_var_store.

aws omics update-variant-store \
    --name my_var_store \
    --description "variant store"

Output:

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "description": "variant store",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "ACTIVE",
    "updateTime": "2022-12-05T18:23:37.686402Z"
}

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

The following code example shows how to use update-workflow.

AWS CLI

To update a workflow

The following update-workflow example updates the description of a workflow with ID 1234567.

aws omics update-workflow \
    --id 1234567 \
    --description "copy workflow"

For more information, see Creating or updating a workflow in the AWS HealthOmics User Guide.

The following code example shows how to use upload-read-set-part.

AWS CLI

To upload a read set part.

The following upload-read-set-part example uploads a specified part of a read set.

aws omics upload-read-set-part \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --part-source SOURCE1 \
    --part-number 1 \
    --payload /path/to/file/read_1_part_1.fastq.gz

Output:

{
    "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635"
}

For more information, see Direct upload to a sequence store in the AWS HealthOmics User Guide.