omics: Amazon Omics

View source: R/omics_service.R

omicsR 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 Accept a resource share request
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 You can optionally create a run group to limit the compute resources for the runs that you add to the group
create_sequence_store Creates a sequence store
create_share Creates a cross-account shared resource
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 resource share
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 the specified resource 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 Retrieves the resource 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)


paws.storage documentation built on Sept. 12, 2024, 6:16 a.m.