AWS HealthOmics MCP Server

Generate, run, debug lifescience workflows.

MCP Info

Attribute	Details
Docker Image	mcp/aws-healthomics-mcp-server
Author	awslabs
Repository	https://github.com/awslabs/mcp

Image Building Info

Attribute	Details
Dockerfile	https://github.com/awslabs/mcp/blob/7bace1f81455088b6690a44e99cabb602259ddf7/src/aws-healthomics-mcp-server/Dockerfile
Commit	`7bace1f81455088b6690a44e99cabb602259ddf7`
Docker Image built by	Docker Inc.
Docker Scout Health Score
Verify Signature	`COSIGN_REPOSITORY=mcp/signatures cosign verify mcp/aws-healthomics-mcp-server --key https://raw.githubusercontent.com/docker/keyring/refs/heads/main/public/mcp/latest.pub`
Licence	Apache License 2.0

Available Tools (22)

Tools provided by this Server	Short Description
`AnalyzeAHORunPerformance`	Analyze AWS HealthOmics workflow run performance and provide optimization recommendations.
`CreateAHOWorkflow`	Create a new HealthOmics workflow.
`CreateAHOWorkflowVersion`	Create a new version of an existing workflow.
`DiagnoseAHORunFailure`	Provides comprehensive diagnostic information for a failed workflow run.
`GetAHORun`	Get details about a specific run.
`GetAHORunEngineLogs`	Retrieve engine logs containing STDOUT and STDERR from the workflow engine process.
`GetAHORunLogs`	Retrieve high-level run logs that show workflow execution events.
`GetAHORunManifestLogs`	Retrieve run manifest logs produced when a workflow completes or fails.
`GetAHORunTask`	Get details about a specific task.
`GetAHOSupportedRegions`	Get the list of AWS regions where HealthOmics is available.
`GetAHOTaskLogs`	Retrieve logs for a specific workflow task containing STDOUT and STDERR.
`GetAHOWorkflow`	Get details about a specific workflow.
`GetSupportedFileTypes`	Get information about supported genomics file types.
`LintAHOWorkflowBundle`	Lint multi-file WDL or CWL workflow bundles and return validation findings.
`LintAHOWorkflowDefinition`	Lint WDL or CWL workflow definitions and return validation findings.
`ListAHORunTasks`	List tasks for a specific run.
`ListAHORuns`	List workflow runs.
`ListAHOWorkflowVersions`	List versions of a workflow.
`ListAHOWorkflows`	List available HealthOmics workflows.
`PackageAHOWorkflow`	Package workflow definition files into a base64-encoded ZIP.
`SearchGenomicsFiles`	Search for genomics files across S3 buckets, HealthOmics sequence stores, and reference stores.
`StartAHORun`	Start a workflow run.

Tools Details

Tool: `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 retrieves detailed manifest logs containing task-level metrics and provides structured data with analysis instructions for AI-powered insights.

Parameters	Type	Description
`run_ids`	`string`	List of run IDs to analyze for resource optimization. Can be provided as a JSON array string like ["run1", "run2"] or as a comma-separated string like "run1,run2"

Tool: `CreateAHOWorkflow`

Create a new HealthOmics workflow.

Parameters	Type	Description
`name`	`string`	Name of the workflow
`container_registry_map`	`string` optional	Optional container registry map with registryMappings (upstreamRegistryUrl, ecrRepositoryPrefix, upstreamRepositoryPrefix, ecrAccountId) and imageMappings (sourceImage, destinationImage) arrays
`container_registry_map_uri`	`string` optional	Optional S3 URI pointing to a JSON file containing container registry mappings. Cannot be used together with container_registry_map
`definition_uri`	`string` optional	S3 URI of the workflow definition ZIP file. Cannot be used together with definition_zip_base64
`definition_zip_base64`	`string` optional	Base64-encoded workflow definition ZIP file. Cannot be used together with definition_uri
`description`	`string` optional	Optional description of the workflow
`parameter_template`	`string` optional	Optional parameter template for the workflow

Tool: `CreateAHOWorkflowVersion`

Create a new version of an existing workflow.

Parameters	Type	Description
`version_name`	`string`	Name for the new version
`workflow_id`	`string`	ID of the workflow
`container_registry_map`	`string` optional	Optional container registry map with registryMappings (upstreamRegistryUrl, ecrRepositoryPrefix, upstreamRepositoryPrefix, ecrAccountId) and imageMappings (sourceImage, destinationImage) arrays
`container_registry_map_uri`	`string` optional	Optional S3 URI pointing to a JSON file containing container registry mappings. Cannot be used together with container_registry_map
`definition_uri`	`string` optional	S3 URI of the workflow definition ZIP file. Cannot be used together with definition_zip_base64
`definition_zip_base64`	`string` optional	Base64-encoded workflow definition ZIP file. Cannot be used together with definition_uri
`description`	`string` optional	Optional description of the workflow version
`parameter_template`	`string` optional	Optional parameter template for the workflow
`storage_capacity`	`string` optional	Storage capacity in GB (required for STATIC)
`storage_type`	`string` optional	Storage type (STATIC or DYNAMIC)

Tool: `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
Task logs from all failed tasks
Actionable recommendations for troubleshooting Parameters|Type|Description -|-|- run_id|string|ID of the failed run

Tool: `GetAHORun`

Get details about a specific run.

Parameters	Type	Description
`run_id`	`string`	ID of the run to retrieve

Tool: `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 Parameters|Type|Description -|-|- run_id|string|ID of the run end_time|string optional|Optional end time for log retrieval (ISO format) limit|integer optional|Maximum number of log events to return next_token|string optional|Token for pagination from a previous response start_from_head|boolean optional|Whether to start from the beginning (True) or end (False) of the log stream start_time|string optional|Optional start time for log retrieval (ISO format)

Tool: `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 Parameters|Type|Description -|-|- run_id|string|ID of the run end_time|string optional|Optional end time for log retrieval (ISO format) limit|integer optional|Maximum number of log events to return next_token|string optional|Token for pagination from a previous response start_from_head|boolean optional|Whether to start from the beginning (True) or end (False) of the log stream start_time|string optional|Optional start time for log retrieval (ISO format)

Tool: `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 Parameters|Type|Description -|-|- run_id|string|ID of the run run_uuid|string|Optional UUID of the run end_time|string optional|Optional end time for log retrieval (ISO format) limit|integer optional|Maximum number of log events to return next_token|string optional|Token for pagination from a previous response start_from_head|boolean optional|Whether to start from the beginning (True) or end (False) of the log stream start_time|string optional|Optional start time for log retrieval (ISO format)

Tool: `GetAHORunTask`

Get details about a specific task.

Parameters	Type	Description
`run_id`	`string`	ID of the run
`task_id`	`string`	ID of the task

Tool: `GetAHOSupportedRegions`

Get the list of AWS regions where HealthOmics is available.

Tool: `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 Parameters|Type|Description -|-|- run_id|string|ID of the run task_id|string|ID of the specific task end_time|string optional|Optional end time for log retrieval (ISO format) limit|integer optional|Maximum number of log events to return next_token|string optional|Token for pagination from a previous response start_from_head|boolean optional|Whether to start from the beginning (True) or end (False) of the log stream start_time|string optional|Optional start time for log retrieval (ISO format)

Tool: `GetAHOWorkflow`

Get details about a specific workflow.

Parameters	Type	Description
`workflow_id`	`string`	ID of the workflow to retrieve
`export_definition`	`boolean` optional	Whether to include a presigned URL for downloading the workflow definition ZIP file

Tool: `GetSupportedFileTypes`

Get information about supported genomics file types.

Tool: `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 Parameters|Type|Description -|-|- main_workflow_file|string|Path to the main workflow file within the bundle workflow_files|object|Dictionary mapping file paths to their content workflow_format|string|The workflow format: 'wdl' or 'cwl'

Tool: `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 Parameters|Type|Description -|-|- workflow_content|string|The workflow definition content to lint workflow_format|string|The workflow format: 'wdl' or 'cwl' filename|string optional|Optional filename for context

Tool: `ListAHORunTasks`

List tasks for a specific run.

Parameters	Type	Description
`run_id`	`string`	ID of the run
`max_results`	`integer` optional	Maximum number of results to return
`next_token`	`string` optional	Token for pagination from a previous response
`status`	`string` optional	Filter by task status

Tool: `ListAHORuns`

List workflow runs.

Parameters	Type	Description
`created_after`	`string` optional	Filter for runs created after this timestamp (ISO format)
`created_before`	`string` optional	Filter for runs created before this timestamp (ISO format)
`max_results`	`integer` optional	Maximum number of results to return
`next_token`	`string` optional	Token for pagination from a previous response
`status`	`string` optional	Filter by run status

Tool: `ListAHOWorkflowVersions`

List versions of a workflow.

Parameters	Type	Description
`workflow_id`	`string`	ID of the workflow
`max_results`	`integer` optional	Maximum number of results to return
`next_token`	`string` optional	Token for pagination from a previous response

Tool: `ListAHOWorkflows`

List available HealthOmics workflows.

Parameters	Type	Description
`max_results`	`integer` optional	Maximum number of results to return
`next_token`	`string` optional	Token for pagination from a previous response

Tool: `PackageAHOWorkflow`

Package workflow definition files into a base64-encoded ZIP.

Parameters	Type	Description
`main_file_content`	`string`	Content of the main workflow file
`additional_files`	`string` optional	Dictionary of additional files (filename: content)
`main_file_name`	`string` optional	Name of the main workflow file

Tool: `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.

Parameters	Type	Description
`continuation_token`	`string` optional	Continuation token from previous search response for paginated results
`enable_storage_pagination`	`boolean` optional	Enable efficient storage-level pagination for large datasets (recommended for >1000 results)
`file_type`	`string` optional	Optional file type filter. Valid types: fastq, fasta, fna, bam, cram, sam, vcf, gvcf, bcf, bed, gff, bai, crai, fai, dict, tbi, csi, bwa_amb, bwa_ann, bwa_bwt, bwa_pac, bwa_sa
`include_associated_files`	`boolean` optional	Whether to include associated files (e.g., BAM index files, FASTQ pairs) in the results
`max_results`	`integer` optional	Maximum number of results to return (1-10000)
`offset`	`integer` optional	Number of results to skip for pagination (0-based offset), ignored if enable_storage_pagination is true
`pagination_buffer_size`	`integer` optional	Buffer size for storage-level pagination (100-50000). Larger values improve ranking accuracy but use more memory.
`search_terms`	`array` optional	List of search terms to match against file paths, tags and metadata. If empty, returns all files of the specified file type.

Tool: `StartAHORun`

Start a workflow run.

Parameters	Type	Description
`name`	`string`	Name for the run
`output_uri`	`string`	S3 URI for the run outputs
`parameters`	`string`	Parameters for the workflow. Parameter names must match one of the keys in the workflow's parameter template.

   All non-optional parameters must be present, if they are not provided the workflow run will not start. No other parameter names are allowed.
   The descriptions of the parameters in the parameter template may provide clues to the type of the parameter. It may be
   necessary to inspect the workflow definition to determine the appropriate parameter type.

Use this MCP Server

{
  "mcpServers": {
    "aws-healthomics": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e",
        "AWS_REGION",
        "-e",
        "AWS_PROFILE",
        "mcp/aws-healthomics-mcp-server"
      ],
      "env": {
        "AWS_REGION": "us-east-1",
        "AWS_PROFILE": "default"
      }
    }
  }
}

Why is it safer to run MCP Servers with Docker?

AWS HealthOmics MCP Server

MCP Info

Image Building Info

Available Tools (22)

Tools Details

Tool: AnalyzeAHORunPerformance

Tool: CreateAHOWorkflow

Tool: CreateAHOWorkflowVersion

Tool: DiagnoseAHORunFailure

Tool: GetAHORun

Tool: GetAHORunEngineLogs

Tool: GetAHORunLogs

Tool: GetAHORunManifestLogs

Tool: GetAHORunTask

Tool: GetAHOSupportedRegions

Tool: GetAHOTaskLogs

Tool: GetAHOWorkflow

Tool: GetSupportedFileTypes

Tool: LintAHOWorkflowBundle

Tool: LintAHOWorkflowDefinition

Tool: ListAHORunTasks

Tool: ListAHORuns

Tool: ListAHOWorkflowVersions

Tool: ListAHOWorkflows

Tool: PackageAHOWorkflow

Tool: SearchGenomicsFiles

Tool: StartAHORun

Use this MCP Server

Tool: `AnalyzeAHORunPerformance`

Tool: `CreateAHOWorkflow`

Tool: `CreateAHOWorkflowVersion`

Tool: `DiagnoseAHORunFailure`

Tool: `GetAHORun`

Tool: `GetAHORunEngineLogs`

Tool: `GetAHORunLogs`

Tool: `GetAHORunManifestLogs`

Tool: `GetAHORunTask`

Tool: `GetAHOSupportedRegions`

Tool: `GetAHOTaskLogs`

Tool: `GetAHOWorkflow`

Tool: `GetSupportedFileTypes`

Tool: `LintAHOWorkflowBundle`

Tool: `LintAHOWorkflowDefinition`

Tool: `ListAHORunTasks`

Tool: `ListAHORuns`

Tool: `ListAHOWorkflowVersions`

Tool: `ListAHOWorkflows`

Tool: `PackageAHOWorkflow`

Tool: `SearchGenomicsFiles`

Tool: `StartAHORun`