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:
- Install uv (Python package manager):
pip install uv
- 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:
- Launch an IES instance using the image:
registry-vpc.miracle.ac.cn/infcprelease/iespro:250217 - Select "Open with VSCode" to access the development environment:
Configuration in Code Server
-
Click the CLINE icon in the left sidebar and configure your LLM model credentials:
-
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
-
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
-
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
-
validate_wdl- Function: Validate WDL workflow script
- Parameters:
- wdl_path: WDL file path
-
generate_inputs- Function: Generate WDL input file template
- Parameters:
- wdl_path: WDL file path
-
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
-
check_build_status- Function: Check Docker image build status
- Parameters:
- task_id: Build task ID
Prompts (Not supported in Cline yet)
-
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
-
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)
-
workflow_input_prompt- Function: Generate workflow input preparation guide
- Content:
- Input file preparation steps
- Parameter validation guidelines
- File path requirements
-
workflow_submission_prompt- Function: Generate workflow submission template
- Content:
- Required credentials (ak/sk)
- Workspace configuration
- Input file requirements
-
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