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Tools
| Name | Description |
|---|---|
ActivateAHOReadSets | Activate archived read sets in a HealthOmics sequence store. Starts an activation job to move read sets from archive storage back to active storage. |
AnalyzeAHORunPerformance | Analyze AWS HealthOmics workflow run performance and provide optimization recommendations. This tool analyzes HealthOmics workflow runs to help users optimize: - Resource utilization patterns (CPU, memory) - Cost optimization opportunities - Performance bottlenecks - Resource allocation efficiency - Runtime optimization suggestions Use this tool when users ask about: - "How can I optimize my HealthOmics runs?" - "Why is my workflow using too many resources?" - "How can I reduce costs for my genomic workflows?" - "What resources are being wasted in my runs?" - "How can I improve workflow performance?" The tool summarizes run manifest logs containing task-level metrics and provides a structured report with recommendations for optimization. |
CancelAHORunBatch | Cancel all runs in a HealthOmics batch. |
CheckContainerAvailability | Check if a container image is available in ECR and accessible by HealthOmics. Queries ECR to determine if a specific container image exists in a repository and whether HealthOmics has the required permissions to pull the image. For pull-through cache repositories, indicates that the image may be pulled on first access even if not currently cached. When initiate_pull_through is True and the image is not found in a pull-through cache repository that is accessible to HealthOmics, this function will attempt to initiate the pull-through using ECR's batch_get_image API call. This triggers ECR to pull the image from the upstream registry and cache it locally. |
CloneContainerToECR | Clone a container image to a private ECR repository for HealthOmics use. This tool copies a container image from an upstream registry (Docker Hub, Quay.io, ECR Public) to your private ECR repository with appropriate HealthOmics access permissions. It uses ECR pull-through cache to perform the copy. The tool will: 1. Parse the source image reference (handling Docker Hub shorthand like "ubuntu:latest") 2. Find an existing pull-through cache rule for the source registry 3. Use the pull-through cache to pull the image into ECR 4. Grant HealthOmics access permissions to the repository 5. Return the ECR URI and digest for use in workflows Image reference formats supported: - "ubuntu:latest" -> registry-1.docker.io/library/ubuntu:latest - "myorg/myimage:v1" -> registry-1.docker.io/myorg/myimage:v1 - "quay.io/biocontainers/samtools:1.17" -> quay.io/biocontainers/samtools:1.17 - "public.ecr.aws/lts/ubuntu:22.04" -> public.ecr.aws/lts/ubuntu:22.04 |
CreateAHOConfiguration | Create a new HealthOmics configuration. |
CreateAHORunCache | Create a new HealthOmics run cache. |
CreateAHORunGroup | Create a new HealthOmics run group. |
CreateAHOSequenceStore | Create a new HealthOmics sequence store. |
CreateAHOWorkflow | Create a new HealthOmics workflow. |
CreateAHOWorkflowVersion | Create a new version of an existing workflow. |
CreateCodeConnection | Create a new CodeConnection. This function creates a new AWS CodeConnection for connecting to a third-party Git provider. The connection will be created in PENDING status and requires OAuth authorization in the AWS Console to become AVAILABLE. |
CreateContainerRegistryMap | Create a container registry map for HealthOmics workflows. Creates a container registry map file that can be used when creating HealthOmics workflows. Registry mappings allow workflows to use container images from upstream registries (Docker Hub, Quay.io, ECR Public) without modifying the workflow definition. The mappings redirect container pulls to your private ECR pull-through caches. By default, this tool discovers all HealthOmics-usable pull-through cache rules in your ECR registry and creates mappings for them. You can also provide additional registry mappings or specific image mappings for container overrides. |
CreatePullThroughCacheForHealthOmics | Create a pull-through cache rule configured for HealthOmics. Creates an ECR pull-through cache rule for the specified upstream registry and configures the necessary permissions for HealthOmics to use it. This includes: 1. Creating the pull-through cache rule 2. Updating the registry permissions policy to allow HealthOmics to create repositories and import images 3. Creating a repository creation template that grants HealthOmics the required permissions to pull images |
DeleteAHOBatch | Delete a HealthOmics batch metadata (does not delete runs). |
DeleteAHOConfiguration | Delete a HealthOmics configuration. |
DeleteAHORunBatch | Delete all runs in a HealthOmics batch. |
DiagnoseAHORunFailure | Provides comprehensive diagnostic information for a failed workflow run. This function collects multiple sources of diagnostic information including: - Run details and failure reason - Engine logs from CloudWatch - Run manifest logs containing workflow summary and resource metrics (when detailed=True) - Task logs from all failed tasks - Actionable recommendations for troubleshooting |
GenerateAHORunTimeline | Generate a Gantt-style timeline visualization for an AWS HealthOmics workflow run. This tool creates an SVG Gantt chart showing task execution phases (pending and running) with status-based coloring. The chart helps visualize task parallelism and identify bottlenecks in workflow execution. Use this tool when users ask about: - "Show me a timeline of my workflow run" - "Visualize the execution of my HealthOmics workflow" - "Create a Gantt chart for my run" - "How did my tasks execute over time?" - "What was the parallelism in my workflow?" The chart displays: - Pending/starting phase (light grey bars) - Running phase (colored by status: blue=COMPLETED, red=FAILED, orange=CANCELLED) - Interactive tooltips with task details (name, CPUs, memory, instance type, cost) - Time axis with configurable units (seconds, minutes, hours, days) |
GetAHOBatch | Get details of a specific HealthOmics batch. |
GetAHOConfiguration | Get details of a specific HealthOmics configuration. |
GetAHOReadSetExportJob | Get details about a read set export job. |
GetAHOReadSetImportJob | Get details about a read set import job. |
GetAHOReadSetMetadata | Get metadata for a specific read set in a HealthOmics sequence store. |
GetAHOReferenceImportJob | Get details about a reference import job. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. |
GetAHOReferenceMetadata | Get metadata for a specific reference in a HealthOmics reference store. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. |
GetAHOReferenceStore | Get details about a specific HealthOmics reference store. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. |
GetAHORun | Get details about a specific run. |
GetAHORunCache | Get details of a specific HealthOmics run cache. |
GetAHORunEngineLogs | Retrieve engine logs containing STDOUT and STDERR from the workflow engine process. These logs contain all output from the workflow engine process including: - Engine startup and initialization messages - Workflow parsing and validation output - Task scheduling and execution messages - Error messages and debugging information |
GetAHORunGroup | Get details of a specific HealthOmics run group. |
GetAHORunLogs | Retrieve high-level run logs that show workflow execution events. These logs contain a high-level summary of events during a run including: - Run creation and start events - File import start and completion - Workflow task start and completion - Export start and completion - Workflow completion |
GetAHORunManifestLogs | Retrieve run manifest logs produced when a workflow completes or fails. These logs contain a summary of the overall workflow including: - Runtime information - Inputs and input digests - Messages and status information - Task summaries with resource allocation and utilization metrics |
GetAHORunTask | Get details about a specific task. |
GetAHOSequenceStore | Get details about a specific HealthOmics sequence store. |
GetAHOSupportedRegions | Get the list of AWS regions where HealthOmics is available. |
GetAHOTaskLogs | Retrieve logs for a specific workflow task containing STDOUT and STDERR. These logs contain the output from a specific task process including: - Task container startup messages - Application-specific output and error messages - Task completion or failure information |
GetAHOWorkflow | Get details about a specific workflow. |
GetCodeConnection | Get details about a specific CodeConnection. This function retrieves detailed information about a specific AWS CodeConnection, including its current status and guidance on next steps. Use this to check if a connection is ready for use with HealthOmics workflows or if OAuth authorization is still required. |
GetSupportedFileTypes | Get information about supported genomics file types. |
GrantHealthOmicsRepositoryAccess | Grant HealthOmics access to an ECR repository. Updates the repository policy to allow the HealthOmics service principal (omics.amazonaws.com) to pull images. This adds the required permissions: - ecr:BatchGetImage - ecr:GetDownloadUrlForLayer If the repository already has a policy, the HealthOmics permissions are added while preserving existing statements. If no policy exists, a new policy is created. |
LintAHOWorkflowBundle | Lint multi-file WDL or CWL workflow bundles and return validation findings. This tool validates multi-file workflow bundles using appropriate linting tools: - WDL workflows: Uses miniwdl package for parsing and validation with import support - CWL workflows: Uses cwltool package for parsing and validation with dependency resolution The tool creates a temporary directory structure that preserves the relative file paths, allowing proper resolution of imports and dependencies between workflow files. The tool checks for: - Syntax errors and parsing issues across all files - Missing required fields (inputs, outputs, steps) - Import/dependency resolution - Runtime requirements for tasks - Common workflow structure issues |
LintAHOWorkflowDefinition | Lint WDL or CWL workflow definitions and return validation findings. This tool validates workflow definitions using appropriate linting tools: - WDL workflows: Uses miniwdl package for parsing and validation - CWL workflows: Uses cwltool package for parsing and validation The tool checks for: - Syntax errors and parsing issues - Missing required fields (inputs, outputs, steps) - Runtime requirements for tasks - Common workflow structure issues |
ListAHOBatches | List HealthOmics batches. |
ListAHOConfigurations | List HealthOmics configurations. |
ListAHOReadSetExportJobs | List read set export jobs for a sequence store. |
ListAHOReadSetImportJobs | List read set import jobs for a sequence store. |
ListAHOReadSets | List read sets in a HealthOmics sequence store with optional filtering. |
ListAHOReferenceImportJobs | List reference import jobs for a reference store. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. |
ListAHOReferenceStores | List HealthOmics reference stores. |
ListAHOReferences | List references in a HealthOmics reference store with optional filtering. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. |
ListAHORunCaches | List HealthOmics run caches. |
ListAHORunGroups | List HealthOmics run groups. |
ListAHORunTasks | List tasks for a specific run. |
ListAHORuns | List workflow runs. |
ListAHORunsInBatch | List runs within a HealthOmics batch. |
ListAHOSequenceStores | List HealthOmics sequence stores. |
ListAHOWorkflowVersions | List versions of a workflow. |
ListAHOWorkflows | List available HealthOmics workflows. |
ListCodeConnections | List available CodeConnections. This function retrieves existing CodeConnections that can be used with HealthOmics workflows. Connections can be filtered by provider type and results are paginated. |
ListECRRepositories | List ECR repositories with HealthOmics accessibility status. Lists all ECR repositories in the current region and checks each repository's policy to determine if HealthOmics has the required permissions to pull images. |
ListPullThroughCacheRules | List pull-through cache rules with HealthOmics usability status. Lists all ECR pull-through cache rules in the current region and evaluates each rule's usability by HealthOmics. A pull-through cache is usable by HealthOmics if: 1. The registry permissions policy grants HealthOmics the required permissions 2. A repository creation template exists for the prefix 3. The template grants HealthOmics the required image pull permissions |
PackageAHOWorkflow | Package workflow definition files into a base64-encoded ZIP. |
SearchGenomicsFiles | Search for genomics files across S3 buckets, HealthOmics sequence stores, and reference stores. This tool provides intelligent search capabilities with pattern matching, file association detection, and ranked results based on relevance scoring. It can find genomics files across multiple storage locations and automatically group related files together. |
StartAHOReadSetExportJob | Start a read set export job to export read sets from a sequence store to S3. |
StartAHOReadSetImportJob | Start a read set import job to import genomic files from S3 into a sequence store. |
StartAHOReferenceImportJob | Start a reference import job to import reference files from S3 into a reference store. AWS HealthOmics allows only one reference store per account per region. If reference_store_id is not provided, it will be automatically resolved. Each source in the sources list is validated against the ReferenceImportSource model and must include: - sourceFile: S3 URI pointing to a FASTA reference file (e.g. "s3://bucket/GRCh38.fasta") - name: A name for the reference (e.g. "GRCh38") - description (optional): A description of the reference - tags (optional): Key-value tags as {"key": "value"} Example sources JSON: [{"sourceFile": "s3://bucket/GRCh38.fasta", "name": "GRCh38", "description": "Human reference genome build 38", "tags": {"build": "38", "species": "human"}}] |
StartAHORun | Start a workflow run. |
StartAHORunBatch | Start a new HealthOmics run batch. |
UpdateAHORunCache | Update an existing HealthOmics run cache. |
UpdateAHORunGroup | Update an existing HealthOmics run group. |
UpdateAHOSequenceStore | Update a HealthOmics sequence store. Internally fetches the current ETag before performing the update to handle optimistic concurrency control. |
ValidateHealthOmicsECRConfig | Validate ECR configuration for HealthOmics workflows. Performs a comprehensive validation of the ECR configuration to ensure HealthOmics workflows can access container images through pull-through caches. This includes checking: 1. All pull-through cache rules in the region 2. Registry permissions policy for HealthOmics principal 3. Repository creation templates for each pull-through cache prefix 4. Template permissions include required actions For each issue found, provides specific remediation steps. |