Client

omics

R Documentation

Amazon Omics¶

Description¶

This is the AWS HealthOmics API Reference. For an introduction to the service, see What is AWS HealthOmics? in the AWS HealthOmics User Guide.

Usage¶

omics(config = list(), credentials = list(), endpoint = NULL, region = NULL)

Arguments¶

config

Optional configuration of credentials, endpoint, and/or region.

credentials:
- creds:
  - access_key_id: AWS access key ID
  - secret_access_key: AWS secret access key
  - session_token: AWS temporary session token
- profile: The name of a profile to use. If not given, then the default profile is used.
- anonymous: Set anonymous credentials.
endpoint: The complete URL to use for the constructed client.
region: The AWS Region used in instantiating the client.
close_connection: Immediately close all HTTP connections.
timeout: The time in seconds till a timeout exception is thrown when attempting to make a connection. The default is 60 seconds.
s3_force_path_style: Set this to true to force the request to use path-style addressing, i.e. ⁠http://s3.amazonaws.com/BUCKET/KEY⁠.
sts_regional_endpoint: Set sts regional endpoint resolver to regional or legacy https://docs.aws.amazon.com/sdkref/latest/guide/feature-sts-regionalized-endpoints.html

credentials

Optional credentials shorthand for the config parameter

creds:
- access_key_id: AWS access key ID
- secret_access_key: AWS secret access key
- session_token: AWS temporary session token
profile: The name of a profile to use. If not given, then the default profile is used.
anonymous: Set anonymous credentials.

endpoint

Optional shorthand for complete URL to use for the constructed client.

region

Optional shorthand for AWS Region used in instantiating the client.

Value¶

A client for the service. You can call the service's operations using syntax like svc$operation(...), where svc is the name you've assigned to the client. The available operations are listed in the Operations section.

Service syntax¶

svc <- omics(
  config = list(
    credentials = list(
      creds = list(
        access_key_id = "string",
        secret_access_key = "string",
        session_token = "string"
      ),
      profile = "string",
      anonymous = "logical"
    ),
    endpoint = "string",
    region = "string",
    close_connection = "logical",
    timeout = "numeric",
    s3_force_path_style = "logical",
    sts_regional_endpoint = "string"
  ),
  credentials = list(
    creds = list(
      access_key_id = "string",
      secret_access_key = "string",
      session_token = "string"
    ),
    profile = "string",
    anonymous = "logical"
  ),
  endpoint = "string",
  region = "string"
)

Operations¶

abort_multipart_read_set_upload: Stops a multipart upload
accept_share: Accepts a share for an analytics store
batch_delete_read_set: Deletes one or more read sets
cancel_annotation_import_job: Cancels an annotation import job
cancel_run: Cancels a run
cancel_variant_import_job: Cancels a variant import job
complete_multipart_read_set_upload: Concludes a multipart upload once you have uploaded all the components
create_annotation_store: Creates an annotation store
create_annotation_store_version: Creates a new version of an annotation store
create_multipart_read_set_upload: Begins a multipart read set upload
create_reference_store: Creates a reference store
create_run_group: Creates a run group
create_sequence_store: Creates a sequence store
create_share: Creates a share offer that can be accepted outside the account by a subscriber
create_variant_store: Creates a variant store
create_workflow: Creates a workflow
delete_annotation_store: Deletes an annotation store
delete_annotation_store_versions: Deletes one or multiple versions of an annotation store
delete_reference: Deletes a genome reference
delete_reference_store: Deletes a genome reference store
delete_run: Deletes a workflow run
delete_run_group: Deletes a workflow run group
delete_sequence_store: Deletes a sequence store
delete_share: Deletes a share of an analytics store
delete_variant_store: Deletes a variant store
delete_workflow: Deletes a workflow
get_annotation_import_job: Gets information about an annotation import job
get_annotation_store: Gets information about an annotation store
get_annotation_store_version: Retrieves the metadata for an annotation store version
get_read_set: Gets a file from a read set
get_read_set_activation_job: Gets information about a read set activation job
get_read_set_export_job: Gets information about a read set export job
get_read_set_import_job: Gets information about a read set import job
get_read_set_metadata: Gets details about a read set
get_reference: Gets a reference file
get_reference_import_job: Gets information about a reference import job
get_reference_metadata: Gets information about a genome reference's metadata
get_reference_store: Gets information about a reference store
get_run: Gets information about a workflow run
get_run_group: Gets information about a workflow run group
get_run_task: Gets information about a workflow run task
get_sequence_store: Gets information about a sequence store
get_share: Retrieves the metadata for a share
get_variant_import_job: Gets information about a variant import job
get_variant_store: Gets information about a variant store
get_workflow: Gets information about a workflow
list_annotation_import_jobs: Retrieves a list of annotation import jobs
list_annotation_stores: Retrieves a list of annotation stores
list_annotation_store_versions: Lists the versions of an annotation store
list_multipart_read_set_uploads: Lists multipart read set uploads and for in progress uploads
list_read_set_activation_jobs: Retrieves a list of read set activation jobs
list_read_set_export_jobs: Retrieves a list of read set export jobs
list_read_set_import_jobs: Retrieves a list of read set import jobs
list_read_sets: Retrieves a list of read sets
list_read_set_upload_parts: This operation will list all parts in a requested multipart upload for a sequence store
list_reference_import_jobs: Retrieves a list of reference import jobs
list_references: Retrieves a list of references
list_reference_stores: Retrieves a list of reference stores
list_run_groups: Retrieves a list of run groups
list_runs: Retrieves a list of runs
list_run_tasks: Retrieves a list of tasks for a run
list_sequence_stores: Retrieves a list of sequence stores
list_shares: Lists all shares associated with an account
list_tags_for_resource: Retrieves a list of tags for a resource
list_variant_import_jobs: Retrieves a list of variant import jobs
list_variant_stores: Retrieves a list of variant stores
list_workflows: Retrieves a list of workflows
start_annotation_import_job: Starts an annotation import job
start_read_set_activation_job: Activates an archived read set
start_read_set_export_job: Exports a read set to Amazon S3
start_read_set_import_job: Starts a read set import job
start_reference_import_job: Starts a reference import job
start_run: Starts a workflow run
start_variant_import_job: Starts a variant import job
tag_resource: Tags a resource
untag_resource: Removes tags from a resource
update_annotation_store: Updates an annotation store
update_annotation_store_version: Updates the description of an annotation store version
update_run_group: Updates a run group
update_variant_store: Updates a variant store
update_workflow: Updates a workflow
upload_read_set_part: This operation uploads a specific part of a read set

Examples¶

## Not run: 
svc <- omics()
svc$abort_multipart_read_set_upload(
  Foo = 123
)

## End(Not run)