drio
Open app

Bio-OS MCP Server

Source

The MCP Servers for Bio-OS instance platforms.

Catalog onlyCatalog onlySTDIO

Overview

Bio-OS MCP Server is a Model Context Protocol (MCP) based tool designed for Bio-OS instance platforms, providing workflow management and Docker image building capabilities.

To use the Bio-OS MCP Server, you can either install it locally using VSCode with the CLINE extension or deploy it in the Miracle Cloud using a pre-configured Docker image. Follow the installation and configuration steps provided in the documentation to get started.

  • Workflow management: Submit, monitor, and validate workflows. - Docker image management: Build and check the status of Docker images. - API reference for various functions related to workflow and Docker management.
  1. Managing and executing complex bioinformatics workflows.
  2. Building and deploying Docker images for bioinformatics applications.
  3. Validating and generating input files for workflows.

Add to your AI client

Use these steps to connect Bio-OS MCP Server in Cursor, Claude, VS Code, and other MCP-compatible apps. The same JSON appears in the Use with menu above for one-click copy.

Cursor

Add this to your .cursor/mcp.json file in your project root, then restart Cursor.

.cursor/mcp.json

{
  "mcpServers": {
    "bioos-mcp-server-gba-bi": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

Claude Desktop

Add this server entry to the mcpServers object in your Claude Desktop config, then restart the app.

~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows)

{
  "mcpServers": {
    "bioos-mcp-server-gba-bi": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

Claude Code

Add this to your project's .mcp.json file. Claude Code will detect it automatically.

.mcp.json (project root)

{
  "mcpServers": {
    "bioos-mcp-server-gba-bi": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

VS Code (Copilot)

Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.

.vscode/mcp.json

{
  "servers": {
    "bioos-mcp-server-gba-bi": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

Windsurf

Add this to your Windsurf MCP config file, then restart Windsurf.

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "bioos-mcp-server-gba-bi": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

Cline

Open Cline settings, navigate to MCP Servers, and add this server configuration.

Cline MCP Settings (via UI)

{
  "mcpServers": {
    "bioos-mcp-server-gba-bi": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-bioos-mcp-server-gba-bi"
      ]
    }
  }
}

FAQ

What are the prerequisites for local installation?

You need to install the Python package manager 'uv' and the Cromwell workflow execution engine.

Can I use Bio-OS MCP Server in the cloud?

Yes! You can deploy it using a pre-configured Docker image in Miracle Cloud.

Is there support for prompts in CLINE?

Currently, prompts are not supported in CLINE but are available when using the MCP server directly.7:["$","div",null,{"className":"container mx-auto flex flex-col gap-4","children":["$L26","$L27",["$","$L28",null,{"currentProject":{"id":1233,"uuid":"adc5afd7-3db2-47a2-b245-40a9df99aeb2","name":"bioos-mcp-server","title":"Bio-OS MCP Server","description":"The MCP Servers for Bio-OS instance platforms.","avatar_url":"https://avatars.githubusercontent.com/u/141196289?v=4","created_at":"2025-02-20T14:05:16.242Z","updated_at":"2025-02-23T07:20:31.500Z","status":"created","author_name":"GBA-BI","author_avatar_url":"https://avatars.githubusercontent.com/u/141196289?v=4","tags":"[]","category":"developer-tools","is_featured":false,"sort":1,"url":"https://github.com/GBA-BI/bioos-mcp-server","target":"_self","content":"$29","summary":"$2a","img_url":"https://github.com/GBA-BI/bioos-mcp-server/raw/main/figures/standalone_configure.png","type":null,"metadata":"{\"star\":\"3\",\"license\":\"MIT license\",\"language\":\"Python\",\"is_official\":false,\"latest_commit_time\":\"2025-04-10 16:23:11\"}","user_uuid":null,"tools":null,"sse_url":null,"sse_provider":null,"sse_params":null,"is_official":false,"server_command":null,"server_params":null,"server_config":null,"allow_call":false,"is_innovation":false,"is_dxt":false,"dxt_manifest":null,"dxt_file_url":null,"is_audit":false},"randomProjects":[],"currentServerKey":"$undefined"}]]}]

Developer tools