AWS HealthOmics

Create, read, update, list and delete sequence-store records.

Plan: Pro107 of 107 operations implemented2Known differences

Sequence-store metadata is verified; genomic data transfer and workflow execution were not verified.

Example checked on Vera 1.2.2, 8 November 2026. Each coverage note names its own evidence and date.

Connect

Activate your license key and start the emulator with the Vera launcher, as in Activate Pro, then run this in a terminal of its own, from an empty scratch directory. It gives the official AWS CLI dummy credentials and a config file of its own, so no AWS account is needed and your own AWS profile isn't touched.

export VERA_ENDPOINT="http://localhost:5003"
export AWS_ACCESS_KEY_ID=test AWS_SECRET_ACCESS_KEY=test
export AWS_REGION=us-east-1 AWS_DEFAULT_REGION=us-east-1
export AWS_SHARED_CREDENTIALS_FILE=/dev/null
export AWS_EC2_METADATA_DISABLED=true
export AWS_PAGER="" AWS_CLI_AUTO_PROMPT=off
unset AWS_PROFILE AWS_DEFAULT_PROFILE
unset AWS_SESSION_TOKEN AWS_SECURITY_TOKEN
unset AWS_WEB_IDENTITY_TOKEN_FILE AWS_ROLE_ARN AWS_ROLE_SESSION_NAME
unset AWS_CONTAINER_CREDENTIALS_FULL_URI
unset AWS_CONTAINER_CREDENTIALS_RELATIVE_URI
cat > vera-aws-config <<'EOF'
[default]
region = us-east-1
output = json
cli_binary_format = base64
s3 =
    addressing_style = path
EOF
export AWS_CONFIG_FILE="$PWD/vera-aws-config"

When you've finished every example in this terminal, close it and delete vera-aws-config, not before.

HealthOmics needs one more setting, in the same terminal. Its operations have host prefixes, such as control-storage- for sequence stores, and this setting stops the AWS CLI from adding them to the endpoint’s host name:

export AWS_DISABLE_HOST_PREFIX_INJECTION=true

Without it, the CLI sends sequence-store requests to a prefixed host, such as http://control-storage-127.0.0.1:5003/sequencestore, and can’t connect. With boto3, Config(inject_host_prefix=False) does the same. The setting is for HealthOmics: it doesn’t help S3 Control, which has a REST example instead.

The example uses the AWS CLI’s omics commands. The emulator serves the 2022-11-28 API over the REST JSON protocol, and the example was checked with the official AWS CLI 2.31.35.

Example

Create a sequence store and read it, then update its description.

STORE_ID=$(aws --endpoint-url "$VERA_ENDPOINT" omics create-sequence-store \
  --name docs-sequences --description 'Documentation sequence metadata' \
  --query id --output text)
aws --endpoint-url "$VERA_ENDPOINT" omics get-sequence-store --id "$STORE_ID"
aws --endpoint-url "$VERA_ENDPOINT" omics update-sequence-store --id "$STORE_ID" \
  --description 'Updated documentation metadata'

The update returns the store with its new description. Its output includes these fields; the store’s id, ARN and times differ on every run, and it also has generated S3 access details:

{
    "name": "docs-sequences",
    "description": "Updated documentation metadata",
    "sseConfig": {
        "type": "KMS"
    },
    "status": "ACTIVE",
    "eTagAlgorithmFamily": "MD5up"
}

The create and get outputs can also have propagatedSetLevelTags, such as omics:sampleId and omics:subjectId, which the update’s output need not.

To clean up, list the stores, then delete this one:

aws --endpoint-url "$VERA_ENDPOINT" omics list-sequence-stores
aws --endpoint-url "$VERA_ENDPOINT" omics delete-sequence-store --id "$STORE_ID"

Supported features

Sequence store records, created with a name and description, read, updated, listed and deleted. A new store is ACTIVE at once, with a KMS encryption setting and generated S3 access details.
Also served, not yet tested: read sets and their multipart uploads, imports, exports and activations, reference stores, variant and annotation stores and their imports, workflows and workflow versions, runs, run groups, run caches and batches, shares, S3 access policies, configurations and tags.

Limitations

The main limits are below. A few more apply to every service, and the API coverage notes cover smaller differences.

No genomic data was transferred. No read-set bytes, imports, exports, genomic parsing or S3 access point operations were checked. A store’s ACTIVE state, KMS setting and S3 URI don’t show that those facilities run. Earlier source inspection, not a run of a release build, found that read-set import jobs complete without importing data.
Workflows weren’t run. No workflow task or container ran. Earlier source inspection, not a run, found that StartRun stores a running workflow record without calling a workflow worker.
Encryption and permissions weren’t tested. KMS keys, role trust, S3 access point policies and quotas weren’t tried.

API coverage

Every operation in AWS's published 2022-11-28 API (SDK model, botocore 1.43.105), and whether the emulator implements it. Availability combines the earlier implementation inventory with the dated observations below; checking a page's example does not verify every operation. Each note names its evidence first; an observation given without a build or date comes from earlier testing, on 3 November 2026. What the statuses mean

Operation	Status	Notes
AbortMultipartReadSetUpload	Implemented
AcceptShare	Implemented
BatchDeleteReadSet	Implemented
CancelAnnotationImportJob	Implemented
CancelRun	Implemented
CancelRunBatch	Implemented
CancelVariantImportJob	Implemented
CompleteMultipartReadSetUpload	Implemented
CreateAnnotationStore	Implemented
CreateAnnotationStoreVersion	Implemented
CreateConfiguration	Implemented
CreateMultipartReadSetUpload	Implemented
CreateReferenceStore	Implemented
CreateRunCache	Implemented
CreateRunGroup	Implemented
CreateSequenceStore	Implemented	Local observation: Vera 1.2.0 preview, 5 November 2026 — created an `ACTIVE` store with a KMS encryption setting and generated S3 access details. Needs `AWS_DISABLE_HOST_PREFIX_INJECTION=true` with the AWS CLI, or the request goes to a prefixed host.
CreateShare	Implemented
CreateVariantStore	Implemented
CreateWorkflow	Implemented
CreateWorkflowVersion	Implemented
DeleteAnnotationStore	Implemented
DeleteAnnotationStoreVersions	Implemented
DeleteBatch	Implemented
DeleteConfiguration	Implemented
DeleteReference	Implemented
DeleteReferenceStore	Implemented
DeleteRun	Implemented
DeleteRunBatch	Implemented
DeleteRunCache	Implemented
DeleteRunGroup	Implemented
DeleteS3AccessPolicy	Implemented
DeleteSequenceStore	Implemented	Local observation: Vera 1.2.0 preview, 5 November 2026 — deleted the store. No read-set data had been stored in it.
DeleteShare	Implemented
DeleteVariantStore	Implemented
DeleteWorkflow	Implemented
DeleteWorkflowVersion	Implemented
GetAnnotationImportJob	Implemented
GetAnnotationStore	Implemented
GetAnnotationStoreVersion	Implemented
GetBatch	Implemented
GetConfiguration	Implemented
GetReadSet	Implemented
GetReadSetActivationJob	Implemented
GetReadSetExportJob	Implemented
GetReadSetImportJob	Implemented
GetReadSetMetadata	Implemented
GetReference	Implemented
GetReferenceImportJob	Implemented
GetReferenceMetadata	Implemented
GetReferenceStore	Implemented
GetRun	Implemented
GetRunCache	Implemented
GetRunGroup	Implemented
GetRunTask	Implemented
GetS3AccessPolicy	Implemented
GetSequenceStore	Implemented	Local observation: Vera 1.2.0 preview, 5 November 2026 — returned the store's name, description and status.
GetShare	Implemented
GetVariantImportJob	Implemented
GetVariantStore	Implemented
GetWorkflow	Implemented
GetWorkflowVersion	Implemented
ListAnnotationImportJobs	Implemented
ListAnnotationStoreVersions	Implemented
ListAnnotationStores	Implemented
ListBatch	Implemented
ListConfigurations	Implemented
ListMultipartReadSetUploads	Implemented
ListReadSetActivationJobs	Implemented
ListReadSetExportJobs	Implemented
ListReadSetImportJobs	Implemented
ListReadSetUploadParts	Implemented
ListReadSets	Implemented
ListReferenceImportJobs	Implemented
ListReferenceStores	Implemented
ListReferences	Implemented
ListRunCaches	Implemented
ListRunGroups	Implemented
ListRunTasks	Implemented
ListRuns	Implemented
ListRunsInBatch	Implemented
ListSequenceStores	Implemented	Local observation: Vera 1.2.0 preview, 5 November 2026 — listed the store.
ListShares	Implemented
ListTagsForResource	Implemented
ListVariantImportJobs	Implemented
ListVariantStores	Implemented
ListWorkflowVersions	Implemented
ListWorkflows	Implemented
PutS3AccessPolicy	Implemented
StartAnnotationImportJob	Implemented
StartReadSetActivationJob	Implemented
StartReadSetExportJob	Implemented
StartReadSetImportJob	Known difference	Source inspection: Immediately records a `COMPLETED` import job and `FINISHED` sources without reading source bytes or importing read-set data.
StartReferenceImportJob	Implemented
StartRun	Known difference	Source inspection: Stores a `RUNNING` workflow record; the inspected path does not call a workflow worker. A running record does not establish workflow execution.
StartRunBatch	Implemented
StartVariantImportJob	Implemented
TagResource	Implemented
UntagResource	Implemented
UpdateAnnotationStore	Implemented
UpdateAnnotationStoreVersion	Implemented
UpdateRunCache	Implemented
UpdateRunGroup	Implemented
UpdateSequenceStore	Implemented	Local observation: Vera 1.2.0 preview, 5 November 2026 — changed the store's description.
UpdateVariantStore	Implemented
UpdateWorkflow	Implemented
UpdateWorkflowVersion	Implemented
UploadReadSetPart	Implemented