# 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):
```bash
pip install uv
```
2. Install Cromwell (Workflow execution engine):
```bash
brew install cromwell
```
#### Installation
Clone the Bio-OS MCP Server repository:
```bash
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:
```json
{
"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
[](https://mcphub.com/mcp-servers/GBA-BI/bioos-mcp-server)
This server is officially certified by [MCPHub](https://mcphub.com/mcp-servers/GBA-BI/bioos-mcp-server). Verify certification status on our MCPHub profile page.
## Contributing
Issues and Pull Requests are welcome.
## License
MIT License
