AWS CLI Command Reference

[ aws . omics ]

create-sequence-store

Description

Creates a sequence store and returns its metadata. Sequence stores are used to store sequence data files called read sets that are saved in FASTQ, BAM, uBAM, or CRAM formats. For aligned formats (BAM and CRAM), a sequence store can only use one reference genome. For unaligned formats (FASTQ and uBAM), a reference genome is not required. You can create multiple sequence stores per region per account.

The following are optional parameters you can specify for your sequence store:

  • Use s3AccessConfig to configure your sequence store with S3 access logs (recommended).
  • Use sseConfig to define your own KMS key for encryption.
  • Use eTagAlgorithmFamily to define which algorithm to use for the HealthOmics eTag on objects.
  • Use fallbackLocation to define a backup location for storing files that have failed a direct upload.
  • Use propagatedSetLevelTags to configure tags that propagate to all objects in your store.

For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide .

See also: AWS API Documentation

Synopsis

  create-sequence-store
--name <value>
[--description <value>]
[--sse-config <value>]
[--tags <value>]
[--client-token <value>]
[--fallback-location <value>]
[--e-tag-algorithm-family <value>]
[--propagated-set-level-tags <value>]
[--s3-access-config <value>]
[--cli-input-json | --cli-input-yaml]
[--generate-cli-skeleton <value>]
[--debug]
[--endpoint-url <value>]
[--no-verify-ssl]
[--no-paginate]
[--output <value>]
[--query <value>]
[--profile <value>]
[--region <value>]
[--version <value>]
[--color <value>]
[--no-sign-request]
[--ca-bundle <value>]
[--cli-read-timeout <value>]
[--cli-connect-timeout <value>]
[--cli-binary-format <value>]
[--no-cli-pager]
[--cli-auto-prompt]
[--no-cli-auto-prompt]

Options

--name (string)

A name for the store.

--description (string)

A description for the store.

--sse-config (structure)

Server-side encryption (SSE) settings for the store.

type -> (string)

The encryption type.

keyArn -> (string)

An encryption key ARN.

Shorthand Syntax:

type=string,keyArn=string

JSON Syntax:

{
  "type": "KMS",
  "keyArn": "string"
}

--tags (map)

Tags for the store. You can configure up to 50 tags.

key -> (string)

value -> (string)

Shorthand Syntax:

KeyName1=string,KeyName2=string

JSON Syntax:

{"string": "string"
  ...}

--client-token (string)

An idempotency token used to dedupe retry requests so that duplicate runs are not created.

--fallback-location (string)

An S3 location that is used to store files that have failed a direct upload. You can add or change the fallbackLocation after creating a sequence store. This is not required if you are uploading files from a different S3 bucket.

--e-tag-algorithm-family (string)

The ETag algorithm family to use for ingested read sets. The default value is MD5up. For more information on ETags, see ETags and data provenance in the Amazon Web Services HealthOmics User Guide .

Possible values:

  • MD5up
  • SHA256up
  • SHA512up

--propagated-set-level-tags (list)

The tags keys to propagate to the S3 objects associated with read sets in the sequence store. These tags can be used as input to add metadata to your read sets.

(string)

Syntax:

"string" "string" ...

--s3-access-config (structure)

S3 access configuration parameters. This specifies the parameters needed to access logs stored in S3 buckets. The S3 bucket must be in the same region and account as the sequence store.

accessLogLocation -> (string)

Location of the access logs.

Shorthand Syntax:

accessLogLocation=string

JSON Syntax:

{
  "accessLogLocation": "string"
}

--cli-input-json | --cli-input-yaml (string) Reads arguments from the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, those values will override the JSON-provided values. It is not possible to pass arbitrary binary values using a JSON-provided value as the string will be taken literally. This may not be specified along with --cli-input-yaml.

--generate-cli-skeleton (string) Prints a JSON skeleton to standard output without sending an API request. If provided with no value or the value input, prints a sample input JSON that can be used as an argument for --cli-input-json. Similarly, if provided yaml-input it will print a sample input YAML that can be used with --cli-input-yaml. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command. The generated JSON skeleton is not stable between versions of the AWS CLI and there are no backwards compatibility guarantees in the JSON skeleton generated.

Global Options

--debug (boolean)

Turn on debug logging.

--endpoint-url (string)

Override command’s default URL with the given URL.

--no-verify-ssl (boolean)

By default, the AWS CLI uses SSL when communicating with AWS services. For each SSL connection, the AWS CLI will verify SSL certificates. This option overrides the default behavior of verifying SSL certificates.

--no-paginate (boolean)

Disable automatic pagination. If automatic pagination is disabled, the AWS CLI will only make one call, for the first page of results.

--output (string)

The formatting style for command output.

  • json
  • text
  • table
  • yaml
  • yaml-stream

--query (string)

A JMESPath query to use in filtering the response data.

--profile (string)

Use a specific profile from your credential file.

--region (string)

The region to use. Overrides config/env settings.

--version (string)

Display the version of this tool.

--color (string)

Turn on/off color output.

  • on
  • off
  • auto

--no-sign-request (boolean)

Do not sign requests. Credentials will not be loaded if this argument is provided.

--ca-bundle (string)

The CA certificate bundle to use when verifying SSL certificates. Overrides config/env settings.

--cli-read-timeout (int)

The maximum socket read time in seconds. If the value is set to 0, the socket read will be blocking and not timeout. The default value is 60 seconds.

--cli-connect-timeout (int)

The maximum socket connect time in seconds. If the value is set to 0, the socket connect will be blocking and not timeout. The default value is 60 seconds.

--cli-binary-format (string)

The formatting style to be used for binary blobs. The default format is base64. The base64 format expects binary blobs to be provided as a base64 encoded string. The raw-in-base64-out format preserves compatibility with AWS CLI V1 behavior and binary values must be passed literally. When providing contents from a file that map to a binary blob fileb:// will always be treated as binary and use the file contents directly regardless of the cli-binary-format setting. When using file:// the file contents will need to properly formatted for the configured cli-binary-format.

  • base64
  • raw-in-base64-out

--no-cli-pager (boolean)

Disable cli pager for output.

--cli-auto-prompt (boolean)

Automatically prompt for CLI input parameters.

--no-cli-auto-prompt (boolean)

Disable automatically prompt for CLI input parameters.

Examples

Note

To use the following examples, you must have the AWS CLI installed and configured. See the Getting started guide in the AWS CLI User Guide for more information.

Unless otherwise stated, all examples have unix-like quotation rules. These examples will need to be adapted to your terminal’s quoting rules. See Using quotation marks with strings in the AWS CLI User Guide .

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.

Output

id -> (string)

The store’s ID.

arn -> (string)

The store’s ARN.

name -> (string)

The store’s name.

description -> (string)

The store’s description.

sseConfig -> (structure)

Server-side encryption (SSE) settings for the store. This contains the KMS key ARN that is used to encrypt read set objects.

type -> (string)

The encryption type.

keyArn -> (string)

An encryption key ARN.

creationTime -> (timestamp)

When the store was created.

fallbackLocation -> (string)

An S3 location that is used to store files that have failed a direct upload.

eTagAlgorithmFamily -> (string)

The algorithm family of the ETag.

status -> (string)

The status of the sequence store.

statusMessage -> (string)

The status message of the sequence store.

propagatedSetLevelTags -> (list)

The tags keys to propagate to the S3 objects associated with read sets in the sequence store.

(string)

s3Access -> (structure)

The S3 access metadata of the sequence store.

s3Uri -> (string)

The S3 URI of the sequence store.

s3AccessPointArn -> (string)

This is ARN of the access point associated with the S3 bucket storing read sets.

accessLogLocation -> (string)

Location of the access logs.
© Copyright 2025, Amazon Web Services. Created using Sphinx.