stdio

stdio MCP servers are not intended to be run remotely, but fly mcp provides the ability to proxy and wrap them.

The data flow is tthat the proxy is a stdio MCP that forwards requests to a wrapper MCP (basically a slimmed down and streamlined Streamable HTTP server), which in turn forwards requests to a stdio MCP running on a remote server:

Start by cloning the MCP servers git repository and making a copy of the Dockerfile:

git clone https://github.com/modelcontextprotocol/servers.git
cd servers
cp src/everything/Dockerfile .

Make the following changes to the Dockerfile:

 RUN npm ci --ignore-scripts --omit-dev
+
+COPY --from=flyio/flyctl /flyctl /usr/bin
+ENTRYPOINT [ "/usr/bin/flyctl", "mcp", "wrap", "--" ]
+EXPOSE 8080

 CMD ["node", "dist/index.js"]

Now run:

fly launch --ha=false

Access the MCP server via the MCP inspector:

fly mcp proxy -i

An example claude_desktop_config.json:

{
  "mcpServers": {
    "filesystem": {
      "command": "/Users/rubys/.fly/bin/flyctl",
      "args": [
         "mcp",
         "proxy",
         "--url=https://mcp.fly.dev/"
       ]
    }
  }
}

Adjust the flyctl path and the value of the --url to match your needs.