OmicsClient
Amazon Web Services HealthOmics is a service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for Amazon Web Services.
For an introduction to the service, see What is Amazon Web Services HealthOmics? in the Amazon Web Services HealthOmics User Guide.
Functions
Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ListMultipartReadSetUploads API operation to view all active multipart read set uploads.
Accept a resource share request.
Deletes one or more read sets. If the operation is successful, it returns a response with no body. If there is an error with deleting one of the read sets, the operation returns an error list. If the operation successfully deletes only a subset of files, it will return an error list for the remaining files that fail to be deleted. There is a limit of 100 read sets that can be deleted in each BatchDeleteReadSet API call.
Cancels an annotation import job.
Cancels a run using its ID and returns a response with no body if the operation is successful. To confirm that the run has been cancelled, use the ListRuns API operation to check that it is no longer listed.
Cancels a variant import job.
Completes a multipart read set upload into a sequence store after you have initiated the upload process with CreateMultipartReadSetUpload and uploaded all read set parts using UploadReadSetPart. You must specify the parts you uploaded using the parts parameter. If the operation is successful, it returns the read set ID(s) of the uploaded read set(s).
Creates an annotation store.
Creates a new version of an annotation store.
Initiates a multipart read set upload for uploading partitioned source files into a sequence store. You can directly import source files from an EC2 instance and other local compute, or from an S3 bucket. To separate these source files into parts, use the split operation. Each part cannot be larger than 100 MB. If the operation is successful, it provides an uploadId which is required by the UploadReadSetPart API operation to upload parts into a sequence store.
Creates a reference store and returns metadata in JSON format. Reference stores are used to store reference genomes in FASTA format. A reference store is created when the first reference genome is imported. To import additional reference genomes from an Amazon S3 bucket, use the StartReferenceImportJob API operation.
Creates a run cache to store and reference task outputs from completed private runs. Specify an Amazon S3 location where Amazon Web Services HealthOmics saves the cached data. This data must be immediately accessible and not in an archived state. You can save intermediate task files to a run cache if they are declared as task outputs in the workflow definition file.
Creates a run group to limit the compute resources for the runs that are added to the group. Returns an ARN, ID, and tags for the run group.
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.
Creates a cross-account shared resource. The resource owner makes an offer to share the resource with the principal subscriber (an AWS user with a different account than the resource owner).
Creates a variant store.
Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:
Creates a new workflow version for the workflow that you specify with the workflowId parameter.
Deletes an annotation store.
Deletes one or multiple versions of an annotation store.
Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the DeleteReferenceStore API operation.
Deletes a reference store and returns a response with no body if the operation is successful. You can only delete a reference store when it does not contain any reference genomes. To empty a reference store, use DeleteReference.
Deletes a run and returns a response with no body if the operation is successful. You can only delete a run that has reached a COMPLETED, FAILED, or CANCELLED stage. A completed run has delivered an output, or was cancelled and resulted in no output. When you delete a run, only the metadata associated with the run is deleted. The run outputs remain in Amazon S3 and logs remain in CloudWatch.
Deletes a run cache and returns a response with no body if the operation is successful. This action removes the cache metadata stored in the service account, but does not delete the data in Amazon S3. You can access the cache data in Amazon S3, for inspection or to troubleshoot issues. You can remove old cache data using standard S3 Delete operations.
Deletes a run group and returns a response with no body if the operation is successful.
Deletes an access policy for the specified store.
Deletes a sequence store and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets.
Deletes a resource share. If you are the resource owner, the subscriber will no longer have access to the shared resource. If you are the subscriber, this operation deletes your access to the share.
Deletes a variant store.
Deletes a workflow by specifying its ID. This operation returns a response with no body if the deletion is successful.
Deletes a workflow version. Deleting a workflow version doesn't affect any ongoing runs that are using the workflow version.
Gets information about an annotation import job.
Gets information about an annotation store.
Retrieves the metadata for an annotation store version.
Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded. You must have read sets uploaded to your sequence store in order to run this operation.
Returns detailed information about the status of a read set activation job in JSON format.
Retrieves status information about a read set export job and returns the data in JSON format. Use this operation to actively monitor the progress of an export job.
Gets detailed and status information about a read set import job and returns the data in JSON format.
Retrieves the metadata for a read set from a sequence store in JSON format. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.
Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded.
Monitors the status of a reference import job. This operation can be called after calling the StartReferenceImportJob operation.
Retrieves metadata for a reference genome. This operation returns the number of parts, part size, and MD5 of an entire file. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.
Gets information about a reference store.
Gets detailed information about a specific run using its ID.
Retrieves detailed information about the specified run cache using its ID.
Gets information about a run group and returns its metadata.
Gets detailed information about a run task using its ID.
Retrieves details about an access policy on a given store.
Retrieves metadata for a sequence store using its ID and returns it in JSON format.
Retrieves the metadata for the specified resource share.
Gets information about a variant import job.
Gets information about a variant store.
Gets all information about a workflow using its ID.
Gets information about a workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Retrieves a list of annotation import jobs.
Retrieves a list of annotation stores.
Lists the versions of an annotation store.
Lists in-progress multipart read set uploads for a sequence store and returns it in a JSON formatted output. Multipart read set uploads are initiated by the CreateMultipartReadSetUploads API operation. This operation returns a response with no body when the upload is complete.
Retrieves a list of read set activation jobs and returns the metadata in a JSON formatted output. To extract metadata from a read set activation job, use the GetReadSetActivationJob API operation.
Retrieves a list of read set export jobs in a JSON formatted response. This API operation is used to check the status of a read set export job initiated by the StartReadSetExportJob API operation.
Retrieves a list of read set import jobs and returns the data in JSON format.
Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format.
Lists all parts in a multipart read set upload for a sequence store and returns the metadata in a JSON formatted output.
Retrieves the metadata of one or more reference import jobs for a reference store.
Retrieves the metadata of one or more reference genomes in a reference store.
Retrieves a list of reference stores linked to your account and returns their metadata in JSON format.
Retrieves a list of your run caches and the metadata for each cache.
Retrieves a list of all run groups and returns the metadata for each run group.
Retrieves a list of runs and returns each run's metadata and status.
Returns a list of tasks and status information within their specified run. Use this operation to monitor runs and to identify which specific tasks have failed.
Retrieves a list of sequence stores and returns each sequence store's metadata.
Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.
Retrieves a list of tags for a resource.
Retrieves a list of variant import jobs.
Retrieves a list of variant stores.
Retrieves a list of existing workflows. You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.
Lists the workflow versions for the specified workflow. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Adds an access policy to the specified store.
Starts an annotation import job.
Activates an archived read set and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the GetReadSetActivationJob operation.
Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the GetReadSetExportJob API operation.
Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the GetReadSetImportJob API operation.
Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the GetReferenceImportJob API operation.
Starts a new run and returns details about the run, or duplicates an existing run. A run is a single invocation of a workflow. If you provide request IDs, Amazon Web Services HealthOmics identifies duplicate requests and starts the run only once. Monitor the progress of the run by calling the GetRun API operation.
Starts a variant import job.
Tags a resource.
Removes tags from a resource.
Updates an annotation store.
Updates the description of an annotation store version.
Updates a run cache using its ID and returns a response with no body if the operation is successful. You can update the run cache description, name, or the default run cache behavior with CACHE_ON_FAILURE or CACHE_ALWAYS. To confirm that your run cache settings have been properly updated, use the GetRunCache API operation.
Updates the settings of a run group and returns a response with no body if the operation is successful.
Update one or more parameters for the sequence store.
Updates a variant store.
Updates information about a workflow.
Updates information about the workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload.
Inherited functions
Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ListMultipartReadSetUploads API operation to view all active multipart read set uploads.
Accept a resource share request.
Deletes one or more read sets. If the operation is successful, it returns a response with no body. If there is an error with deleting one of the read sets, the operation returns an error list. If the operation successfully deletes only a subset of files, it will return an error list for the remaining files that fail to be deleted. There is a limit of 100 read sets that can be deleted in each BatchDeleteReadSet API call.
Cancels an annotation import job.
Cancels a run using its ID and returns a response with no body if the operation is successful. To confirm that the run has been cancelled, use the ListRuns API operation to check that it is no longer listed.
Cancels a variant import job.
Completes a multipart read set upload into a sequence store after you have initiated the upload process with CreateMultipartReadSetUpload and uploaded all read set parts using UploadReadSetPart. You must specify the parts you uploaded using the parts parameter. If the operation is successful, it returns the read set ID(s) of the uploaded read set(s).
Creates an annotation store.
Creates a new version of an annotation store.
Initiates a multipart read set upload for uploading partitioned source files into a sequence store. You can directly import source files from an EC2 instance and other local compute, or from an S3 bucket. To separate these source files into parts, use the split operation. Each part cannot be larger than 100 MB. If the operation is successful, it provides an uploadId which is required by the UploadReadSetPart API operation to upload parts into a sequence store.
Creates a reference store and returns metadata in JSON format. Reference stores are used to store reference genomes in FASTA format. A reference store is created when the first reference genome is imported. To import additional reference genomes from an Amazon S3 bucket, use the StartReferenceImportJob API operation.
Creates a run cache to store and reference task outputs from completed private runs. Specify an Amazon S3 location where Amazon Web Services HealthOmics saves the cached data. This data must be immediately accessible and not in an archived state. You can save intermediate task files to a run cache if they are declared as task outputs in the workflow definition file.
Creates a run group to limit the compute resources for the runs that are added to the group. Returns an ARN, ID, and tags for the run group.
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.
Creates a cross-account shared resource. The resource owner makes an offer to share the resource with the principal subscriber (an AWS user with a different account than the resource owner).
Creates a variant store.
Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:
Creates a new workflow version for the workflow that you specify with the workflowId parameter.
Deletes an annotation store.
Deletes one or multiple versions of an annotation store.
Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the DeleteReferenceStore API operation.
Deletes a reference store and returns a response with no body if the operation is successful. You can only delete a reference store when it does not contain any reference genomes. To empty a reference store, use DeleteReference.
Deletes a run and returns a response with no body if the operation is successful. You can only delete a run that has reached a COMPLETED, FAILED, or CANCELLED stage. A completed run has delivered an output, or was cancelled and resulted in no output. When you delete a run, only the metadata associated with the run is deleted. The run outputs remain in Amazon S3 and logs remain in CloudWatch.
Deletes a run cache and returns a response with no body if the operation is successful. This action removes the cache metadata stored in the service account, but does not delete the data in Amazon S3. You can access the cache data in Amazon S3, for inspection or to troubleshoot issues. You can remove old cache data using standard S3 Delete operations.
Deletes a run group and returns a response with no body if the operation is successful.
Deletes an access policy for the specified store.
Deletes a sequence store and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets.
Deletes a resource share. If you are the resource owner, the subscriber will no longer have access to the shared resource. If you are the subscriber, this operation deletes your access to the share.
Deletes a variant store.
Deletes a workflow by specifying its ID. This operation returns a response with no body if the deletion is successful.
Deletes a workflow version. Deleting a workflow version doesn't affect any ongoing runs that are using the workflow version.
Gets information about an annotation import job.
Gets information about an annotation store.
Retrieves the metadata for an annotation store version.
Returns detailed information about the status of a read set activation job in JSON format.
Retrieves status information about a read set export job and returns the data in JSON format. Use this operation to actively monitor the progress of an export job.
Gets detailed and status information about a read set import job and returns the data in JSON format.
Retrieves the metadata for a read set from a sequence store in JSON format. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.
Monitors the status of a reference import job. This operation can be called after calling the StartReferenceImportJob operation.
Retrieves metadata for a reference genome. This operation returns the number of parts, part size, and MD5 of an entire file. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.
Gets information about a reference store.
Gets detailed information about a specific run using its ID.
Retrieves detailed information about the specified run cache using its ID.
Gets information about a run group and returns its metadata.
Gets detailed information about a run task using its ID.
Retrieves details about an access policy on a given store.
Retrieves metadata for a sequence store using its ID and returns it in JSON format.
Retrieves the metadata for the specified resource share.
Gets information about a variant import job.
Gets information about a variant store.
Gets all information about a workflow using its ID.
Gets information about a workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Retrieves a list of annotation import jobs.
Paginate over ListAnnotationImportJobsResponse results.
Retrieves a list of annotation stores.
Paginate over ListAnnotationStoresResponse results.
Lists the versions of an annotation store.
Paginate over ListAnnotationStoreVersionsResponse results.
Lists in-progress multipart read set uploads for a sequence store and returns it in a JSON formatted output. Multipart read set uploads are initiated by the CreateMultipartReadSetUploads API operation. This operation returns a response with no body when the upload is complete.
Paginate over ListMultipartReadSetUploadsResponse results.
Retrieves a list of read set activation jobs and returns the metadata in a JSON formatted output. To extract metadata from a read set activation job, use the GetReadSetActivationJob API operation.
Paginate over ListReadSetActivationJobsResponse results.
Retrieves a list of read set export jobs in a JSON formatted response. This API operation is used to check the status of a read set export job initiated by the StartReadSetExportJob API operation.
Paginate over ListReadSetExportJobsResponse results.
Retrieves a list of read set import jobs and returns the data in JSON format.
Paginate over ListReadSetImportJobsResponse results.
Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format.
Paginate over ListReadSetsResponse results.
Lists all parts in a multipart read set upload for a sequence store and returns the metadata in a JSON formatted output.
Paginate over ListReadSetUploadPartsResponse results.
Retrieves the metadata of one or more reference import jobs for a reference store.
Paginate over ListReferenceImportJobsResponse results.
Retrieves the metadata of one or more reference genomes in a reference store.
Paginate over ListReferencesResponse results.
Retrieves a list of reference stores linked to your account and returns their metadata in JSON format.
Paginate over ListReferenceStoresResponse results.
Retrieves a list of your run caches and the metadata for each cache.
Paginate over ListRunCachesResponse results.
Retrieves a list of all run groups and returns the metadata for each run group.
Paginate over ListRunGroupsResponse results.
Retrieves a list of runs and returns each run's metadata and status.
Paginate over ListRunsResponse results.
Returns a list of tasks and status information within their specified run. Use this operation to monitor runs and to identify which specific tasks have failed.
Paginate over ListRunTasksResponse results.
Retrieves a list of sequence stores and returns each sequence store's metadata.
Paginate over ListSequenceStoresResponse results.
Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.
Paginate over ListSharesResponse results.
Retrieves a list of tags for a resource.
Retrieves a list of variant import jobs.
Paginate over ListVariantImportJobsResponse results.
Retrieves a list of variant stores.
Paginate over ListVariantStoresResponse results.
Retrieves a list of existing workflows. You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.
Paginate over ListWorkflowsResponse results.
Lists the workflow versions for the specified workflow. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Paginate over ListWorkflowVersionsResponse results.
Adds an access policy to the specified store.
Starts an annotation import job.
Activates an archived read set and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the GetReadSetActivationJob operation.
Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the GetReadSetExportJob API operation.
Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the GetReadSetImportJob API operation.
Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the GetReferenceImportJob API operation.
Starts a new run and returns details about the run, or duplicates an existing run. A run is a single invocation of a workflow. If you provide request IDs, Amazon Web Services HealthOmics identifies duplicate requests and starts the run only once. Monitor the progress of the run by calling the GetRun API operation.
Starts a variant import job.
Tags a resource.
Removes tags from a resource.
Updates an annotation store.
Updates the description of an annotation store version.
Updates a run cache using its ID and returns a response with no body if the operation is successful. You can update the run cache description, name, or the default run cache behavior with CACHE_ON_FAILURE or CACHE_ALWAYS. To confirm that your run cache settings have been properly updated, use the GetRunCache API operation.
Updates the settings of a run group and returns a response with no body if the operation is successful.
Update one or more parameters for the sequence store.
Updates a variant store.
Updates information about a workflow.
Updates information about the workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload.
Wait until an annotation import is completed
Wait until an annotation store is created
Wait until an annotation store is deleted.
Wait until an annotation store version is created
Wait until an annotation store version is deleted.
Wait until a job is completed.
Wait until a job is completed.
Wait until a job is completed.
Wait until a job is completed.
Wait until a run is completed.
Wait until a run is running.
Wait until a task is completed.
Wait until a task is running.
Wait until variant import is completed
Wait until a variant store is created
Wait until a variant store is deleted.
Wait until a workflow is active.
Wait until a workflow version is active.
Create a copy of the client with one or more configuration values overridden. This method allows the caller to perform scoped config overrides for one or more client operations.