AWS CLI Command Reference

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[ aws . omics ]

start-annotation-import-job

Description

Starts an annotation import job.

See also: AWS API Documentation

Synopsis

  start-annotation-import-job
--destination-name <value>
--role-arn <value>
--items <value>
[--version-name <value>]
[--format-options <value>]
[--run-left-normalization | --no-run-left-normalization]
[--annotation-fields <value>]
[--cli-input-json <value>]
[--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>]

Options

--destination-name (string)

A destination annotation store for the job.

--role-arn (string)

A service role for the job.

--items (list)

Items to import.

(structure)

A source for an annotation import job.

source -> (string)

The source file's location in Amazon S3.

Shorthand Syntax:

source=string ...

JSON Syntax:

[
  {
    "source": "string"
  }
  ...
]

--version-name (string)

The name of the annotation store version.

--format-options (tagged union structure)

Formatting options for the annotation file.

Note

This is a Tagged Union structure. Only one of the following top level keys can be set: tsvOptions, vcfOptions.

tsvOptions -> (structure)

Options for a TSV file.

readOptions -> (structure)

The file's read options.

sep -> (string)

The file's field separator.

encoding -> (string)

The file's encoding.

quote -> (string)

The file's quote character.

quoteAll -> (boolean)

Whether all values need to be quoted, or just those that contain quotes.

escape -> (string)

A character for escaping quotes in the file.

escapeQuotes -> (boolean)

Whether quotes need to be escaped in the file.

comment -> (string)

The file's comment character.

header -> (boolean)

Whether the file has a header row.

lineSep -> (string)

A line separator for the file.

vcfOptions -> (structure)

Options for a VCF file.

ignoreQualField -> (boolean)

The file's ignore qual field setting.

ignoreFilterField -> (boolean)

The file's ignore filter field setting.

Shorthand Syntax:

tsvOptions={readOptions={sep=string,encoding=string,quote=string,quoteAll=boolean,escape=string,escapeQuotes=boolean,comment=string,header=boolean,lineSep=string}},vcfOptions={ignoreQualField=boolean,ignoreFilterField=boolean}

JSON Syntax:

{
  "tsvOptions": {
    "readOptions": {
      "sep": "string",
      "encoding": "string",
      "quote": "string",
      "quoteAll": true|false,
      "escape": "string",
      "escapeQuotes": true|false,
      "comment": "string",
      "header": true|false,
      "lineSep": "string"
    }
  },
  "vcfOptions": {
    "ignoreQualField": true|false,
    "ignoreFilterField": true|false
  }
}

--run-left-normalization | --no-run-left-normalization (boolean)

The job's left normalization setting.

--annotation-fields (map)

The annotation schema generated by the parsed annotation data.

key -> (string)

value -> (string)

Shorthand Syntax:

KeyName1=string,KeyName2=string

JSON Syntax:

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

--cli-input-json (string) Performs service operation based on the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, the CLI 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.

--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. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command.

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.

--output (string)

The formatting style for command output.

  • json
  • text
  • table

--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.

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 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.

Output

jobId -> (string)

The job's ID.