Bio-OS MCP Server

A Model Context Protocol (MCP) based tool and prompt server for Bio-OS that provides workflow management and Docker image building capabilities.

Usage

We recommend using the CLINE extension for VSCode to interact with this MCP tool. There are two deployment options available: standalone installation on your local machine or using Code Server in a Miracle Cloud IES instance. Choose the option that best suits your needs.

Local Installation (Using MCP through local VSCode)

Prerequisites

Bio-OS MCP Server requires the following dependencies:

1. Install uv (Python package manager):

pip install uv

2. Install Cromwell (Workflow execution engine):

brew install cromwell

Installation

Clone the Bio-OS MCP Server repository:

git clone https://github.com/GBA-BI/bioos-mcp-server.git

Configuration

Configure the Bio-OS MCP Server script path in CLINE's MCP settings. Replace the placeholders with absolute paths to your installation:

{
  "mcpServers": {
    "bioos": {
      "command": "path/to/uv",
      "args": [
        "--directory",
        "path/to/bioos-mcp-server",
        "run",
        "path/to/bioos-mcp-server/src/bioos_mcp/bioos_mcp_server.py"
      ],
      "env": {
        "PYTHONPATH": "path/to/bioos-mcp-server/src",
        "MIRACLE_ACCESS_KEY": "xxxxxxxxxxxx",
        "MIRACLE_SECRET_KEY": "xxxxxxxxxxxx"
      }
    }
  }
} 

Follow the configuration process shown below. The Bio-OS MCP Server is ready to use when the status turns green. If the connection is unstable, click "Retry Connection":

Since CLINE does not yet support MCP Prompts, copy the contents of bioos-mcp-prompt.md into CLINE's Custom Instructions for optimal experience:

After completing the configuration, you can begin using the Bio-OS MCP Server for development.

Cloud Installation (Using MCP through Code Server in Miracle Cloud)

For Miracle Cloud users, we provide a pre-configured Docker image with all Bio-OS MCP Server dependencies. Follow these steps:

1. Launch an IES instance using the image: registry-vpc.miracle.ac.cn/infcprelease/iespro:250217
2. Select "Open with VSCode" to access the development environment:

Configuration in Code Server

1. Click the CLINE icon in the left sidebar and configure your LLM model credentials:

2. Navigate to CLINE's MCP configuration page and verify that Bio-OS MCP Server is properly connected. Use "Retry Connection" if needed:

Once configured, you can begin development with Bio-OS MCP Server.

Features

1. Workflow Management

• Submit and monitor workflows
• Upload WDL workflows
• Validate WDL scripts
• Generate input file templates

2. Docker Image Management

• Build Docker images
• Check build status
• Monitor build progress
• Retrieve build logs

API Reference

Tools

1. submit_workflow

   • Function: Submit Bio-OS workflow
   • Parameters:
     • ak: Access Key
     • sk: Secret Key
     • workspace_name: Workspace name
     • workflow_name: Workflow name
     • input_json: Input JSON file path

2. import_workflow

   • Function: Upload WDL workflow to Bio-OS system
   • Parameters:
     • ak: Access Key
     • sk: Secret Key
     • workspace_name: Workspace name
     • workflow_name: Workflow name
     • workflow_source: WDL file path
     • workflow_desc: Workflow description

3. validate_wdl

   • Function: Validate WDL workflow script
   • Parameters:
     • wdl_path: WDL file path

4. generate_inputs

   • Function: Generate WDL input file template
   • Parameters:
     • wdl_path: WDL file path

5. build_docker_image

   • Function: Build Docker image
   • Parameters:
     • registry: Image registry address
     • namespace_name: Namespace
     • repo_name: Repository name
     • tag: Version tag
     • source_path: Dockerfile or archive path

6. check_build_status

   • Function: Check Docker image build status
   • Parameters:
     • task_id: Build task ID

Prompts (Not supported in Cline yet)

1. wdl_development_workflow_prompt

   • Function: Generate complete guidance for WDL workflow development
   • Content:
     • WDL script development steps
     • Task structure guidelines
     • Runtime configuration requirements
     • Docker image preparation guide

2. wdl_runtime_prompt

   • Function: Generate WDL runtime configuration template
   • Content:
     • Required docker image configuration
     • Memory settings (default: 8 GB)
     • Disk settings (default: 20 GB)
     • CPU settings (default: 4)

3. workflow_input_prompt

   • Function: Generate workflow input preparation guide
   • Content:
     • Input file preparation steps
     • Parameter validation guidelines
     • File path requirements

4. workflow_submission_prompt

   • Function: Generate workflow submission template
   • Content:
     • Required credentials (ak/sk)
     • Workspace configuration
     • Input file requirements

5. docker_build_prompt

   • Function: Generate Docker build process guide
   • Content:
     • Dockerfile generation steps
     • Build configuration requirements
     • Image registry settings
     • Build status monitoring guide

Note: Prompts are currently not supported in Cline environment. These prompts are only available when using the MCP server directly or through Claude Desktop.

✅ Certified by MCPHub

This server is officially certified by MCPHub. Verify certification status on our MCPHub profile page.

Contributing

Issues and Pull Requests are welcome.

License

MIT License