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"
      }
    }
  }
} 

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:

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

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.

Contributing

Issues and Pull Requests are welcome.

License

MIT License