Docker's MCP Toolkit is a great way to expose Model Context Protocol servers to AI clients like Claude, n8n, or Cursor. Out of the box it's designed for Docker Desktop on macOS and Windows — but what if you want to run it on a headless Linux server? A Raspberry Pi, a VPS, a home lab box? This guide walks through setting it up from scratch on Linux (Debian/Ubuntu, arm64 or amd64), including secrets management, custom MCP server images, and a systemd service that starts automatically on boot. > This guide is based on getting it actually working on a Raspberry Pi 5 running > Debian 13. Several things that look like they should work on Linux don't — I'll > call those out explicitly so you don't waste time on the same dead ends. --- ## What We're Building A self-hosted MCP gateway that: - Runs any MCP server as a Docker container - Exposes them all behind a single HTTP endpoint with Bearer token auth - Starts automatically on boot via systemd ```plaintext AI Client → http://your-server:8811/sse → docker-mcp gateway → MCP containers ``` --- ## Prerequisites - Linux host with Docker installed (Docker Engine, not Docker Desktop) - Your user in the `docker` group (`sudo usermod -aG docker $USER`) - SSH access if setting up remotely --- ## Step 1 — Install the docker-mcp Binary The `docker mcp` command is a Docker CLI plugin. On Linux you install it directly from the GitHub releases — no Docker Desktop needed. ```bash # Create the CLI plugins directory sudo mkdir -p /usr/local/lib/docker/cli-plugins # Download the binary for your architecture # arm64 (Raspberry Pi 4/5, Apple Silicon VMs): sudo curl -fsSL \ https://github.com/docker/mcp-gateway/releases/download/v0.41.0/docker-mcp-linux-arm64.tar.gz \ | sudo tar -xz -C /usr/local/lib/docker/cli-plugins/ # amd64 (regular x86 server): sudo curl -fsSL \ https://github.com/docker/mcp-gateway/releases/download/v0.41.0/docker-mcp-linux-amd64.tar.gz \ | sudo tar -xz -C /usr/local/lib/docker/cli-plugins/ sudo chmod +x /usr/local/lib/docker/cli-plugins/docker-mcp # Verify docker mcp --version ``` Check the [releases page](https://github.com/docker/mcp-gateway/releases) for the latest version. --- ## Step 2 — The docker-pass Workaround This is the first Linux-specific gotcha. `docker mcp` CLI commands (like `docker mcp server ls`) expect a Docker CLI plugin named `docker-pass`. This binary ships with Docker Desktop on macOS but not on Linux, causing this error: ```plaintext docker pass has not been installed ``` The fix: a small wrapper script that satisfies the Docker CLI plugin protocol and delegates to `docker-credential-pass`. First, install `docker-credential-pass`: ```bash # arm64: sudo curl -fsSL \ https://github.com/docker/docker-credential-helpers/releases/download/v0.9.5/docker-credential-pass-v0.9.5.linux-arm64 \ -o /usr/local/bin/docker-credential-pass # amd64: sudo curl -fsSL \ https://github.com/docker/docker-credential-helpers/releases/download/v0.9.5/docker-credential-pass-v0.9.5.linux-amd64 \ -o /usr/local/bin/docker-credential-pass sudo chmod +x /usr/local/bin/docker-credential-pass ``` Then create the wrapper plugin: ```bash sudo tee /usr/local/lib/docker/cli-plugins/docker-pass > /dev/null << 'EOF' #!/bin/bash if [[ "$1" == "docker-cli-plugin-metadata" ]]; then echo '{"SchemaVersion":"0.1.0","Vendor":"Docker","Version":"v1.0.0","ShortDescription":"Docker Pass secrets helper"}' exit 0 fi exec docker-credential-pass "$@" EOF sudo chmod +x /usr/local/lib/docker/cli-plugins/docker-pass ``` Verify Docker recognizes it: ```bash docker info --format '{{.ClientInfo.Plugins}}' | tr ',' '\n' | grep pass # Should show: ...pass /usr/local/lib/docker/cli-plugins/docker-pass... ``` > **Note**: This wrapper is only needed for `docker mcp` CLI commands. The gateway > itself uses a different mechanism for secrets — covered in Step 5. --- ## Step 3 — Pull or Load Your MCP Images Any Docker image that implements the MCP stdio protocol can be used as an MCP server. ### Option A: Images from the official Docker MCP catalog ```bash docker pull mcp/playwright:latest ``` ### Option B: Custom/private images Transfer from another machine: ```bash # On the source machine: docker save mcp/my-server:latest | ssh your-linux-host "docker load" ``` --- ## Step 4 — Configure the Gateway Create the config directory: ```bash mkdir -p ~/.docker/mcp/catalogs ``` ### registry.yaml — which servers to enable ```bash cat > ~/.docker/mcp/registry.yaml << 'EOF' registry: playwright: ref: "" my-server: ref: "" EOF ``` ### catalog.json — where to find catalog definitions The gateway needs to know where your catalog files live. By default it only reads the official Docker MCP catalog. Register additional catalogs here: ```bash cat > ~/.docker/mcp/catalog.json << 'EOF' { "catalogs": { "docker-mcp": { "displayName": "Docker MCP Catalog", "url": "https://desktop.docker.com/mcp/catalog/v2/catalog.yaml" }, "my-catalog": { "displayName": "My Custom Servers", "url": "/home/youruser/.docker/mcp/catalogs/my-catalog.yaml" } } } EOF ``` ### A catalog YAML for a custom server The catalog defines how a server runs and which env vars it needs. List **all** env vars under `secrets:` — including non-sensitive ones like usernames. > **Linux gotcha**: The `config:` field in catalog YAMLs is not used for env var > injection on Linux. Everything must be in `secrets:` to be passed to containers. ```yaml registry: my-server: title: My MCP Server description: Does something useful image: mcp/my-server:latest type: server tools: [] secrets: - name: my-server.api_key env: API_KEY description: API key for the service - name: my-server.username env: USERNAME description: Your username name: my-catalog displayName: My Catalog ``` --- ## Step 5 — Secrets This is the second major Linux gotcha. `docker mcp` uses a secrets engine (`se://` URIs) that is Docker Desktop-only and doesn't work on Linux. The `docker mcp secret set` command will fail with `docker pass has not been installed` even after you install the wrapper from Step 2. The solution is the `--secrets` flag, which points the gateway at a plain env file: ```bash # Create the secrets file cat > ~/.docker/mcp/secrets.env << 'EOF' my-server.api_key=your-api-key-here my-server.username=your-username EOF # Restrict permissions — only your user can read it chmod 600 ~/.docker/mcp/secrets.env ``` The key names map to the `name` field in the catalog's `secrets:` list. **Is this secure?** The file is `chmod 600` — readable only by your user, same as `~/.ssh/id_rsa`. Anyone who can read it already has root or is you. If you want GPG encryption at rest, you can store sensitive values in `pass` and populate the file from it — but for an unattended service the threat model is the same either way. **Are secrets isolated between MCP servers?** Yes, completely. The secrets file is never passed to or mounted into any container. The gateway reads it internally and uses it purely as a lookup table. When spawning each container it passes only the specific `-e VAR=value` flags declared in that server's catalog `secrets:` list. You can verify this with `--dry-run --verbose` — the `docker run` command for each server is logged in full, and you'll see that playwright gets zero secret env vars, while my-server only gets `USERNAME` and `API_KEY`. There is no way for one MCP server to access another's credentials. --- ## Step 6 — Test the Gateway Do a dry run first: ```bash docker mcp gateway run \ --dry-run \ --verbose \ --secrets ~/.docker/mcp/secrets.env \ 2>&1 ``` You should see all your configured servers listed and their tools counted, with no `Warning: Secret '...' not found` lines. If warnings appear, check that the key names in `secrets.env` exactly match the `name` fields in your catalog YAML. If everything looks good, start it live: ```bash docker mcp gateway run \ --transport sse \ --port 8811 \ --secrets ~/.docker/mcp/secrets.env ``` --- ## Step 7 — systemd Service Create the service file: ```bash sudo tee /etc/systemd/system/mcp-gateway.service > /dev/null << EOF [Unit] Description=Docker MCP Gateway Requires=docker.service After=docker.service network-online.target Wants=network-online.target [Service] Type=simple User=$(whoami) Environment=HOME=$HOME ExecStart=/usr/local/lib/docker/cli-plugins/docker-mcp gateway run \\ --transport sse \\ --port 8811 \\ --secrets $HOME/.docker/mcp/secrets.env Restart=on-failure RestartSec=10 [Install] WantedBy=multi-user.target EOF ``` Set a stable Bearer token that survives restarts: ```bash sudo mkdir -p /etc/systemd/system/mcp-gateway.service.d TOKEN=$(openssl rand -hex 32) echo "Save this token: $TOKEN" sudo tee /etc/systemd/system/mcp-gateway.service.d/token.conf > /dev/null << EOF [Service] Environment=MCP_GATEWAY_AUTH_TOKEN=$TOKEN EOF ``` Without this, the gateway generates a new random token on every start — which means reconfiguring every client after each restart. Enable and start: ```bash sudo systemctl daemon-reload sudo systemctl enable mcp-gateway.service sudo systemctl start mcp-gateway.service ``` Check it's running: ```bash sudo systemctl status mcp-gateway.service journalctl -u mcp-gateway.service -f ``` --- ## Connecting a Client The gateway runs on port `8811` with SSE transport: ```http URL: http://your-server:8811/sse Auth: Authorization: Bearer ``` ### Claude Desktop Add to `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) or the equivalent on your OS: ```json { "mcpServers": { "my-gateway": { "command": "npx", "args": [ "mcp-remote", "http://your-server:8811/sse", "--header", "Authorization: Bearer ", "--allow-http", "--transport", "sse-only" ] } } } ``` Two flags are required here that aren't obvious: - `--allow-http` — `mcp-remote` blocks non-HTTPS URLs by default - `--transport sse-only` — the default `http-first` strategy sends a POST that the gateway rejects with `sessionid must be provided` --- ## Troubleshooting ### `docker pass has not been installed` The `docker-pass` CLI plugin wrapper is missing or not executable. Re-check Step 2. ### `Warning: Secret '...' not found` The key name in `secrets.env` doesn't match the `name` field in the catalog YAML, or you forgot to pass `--secrets` to the gateway. Check with: ```bash docker mcp gateway run --dry-run --verbose --secrets ~/.docker/mcp/secrets.env 2>&1 | grep Warning ``` ### Server shows 0 tools in dry-run but works live Some servers need the actual secrets present to respond to tool listing. This is normal — the gateway still starts them correctly at runtime. ### `cannot use --port with --transport=stdio` You must specify `--transport sse` when using `--port`. The default transport is stdio (for direct client connections), not HTTP. ### `sessionid must be provided` in mcp-remote Add `--transport sse-only` to the `mcp-remote` args. The default transport strategy tries Streamable HTTP first, which the gateway doesn't support. --- ## Keeping Things Updated ### Upgrade docker-mcp ```bash VERSION=v0.41.0 # replace with latest ARCH=arm64 # or amd64 sudo curl -fsSL \ https://github.com/docker/mcp-gateway/releases/download/$VERSION/docker-mcp-linux-$ARCH.tar.gz \ | sudo tar -xz -C /usr/local/lib/docker/cli-plugins/ sudo chmod +x /usr/local/lib/docker/cli-plugins/docker-mcp sudo systemctl restart mcp-gateway.service ``` ### Update a custom MCP image ```bash docker save mcp/my-server:latest | ssh your-linux-host "docker load" ssh your-linux-host "sudo systemctl restart mcp-gateway.service" ``` --- ## Summary The key differences from macOS Docker Desktop: | Concern | macOS (Docker Desktop) | Linux (headless) | |---|---|---| | `docker-mcp` binary | Bundled with Docker Desktop | Downloaded from GitHub releases | | `docker-pass` plugin | Proprietary binary | Wrapper script → `docker-credential-pass` | | Secrets injection | `docker mcp secret set` + keychain | `--secrets ` (chmod 600) | | Auto-start | Docker Desktop | systemd service | | Transport | stdio or SSE | SSE with `--transport sse` | | mcp-remote | Default settings work | Needs `--allow-http --transport sse-only` | Everything else — catalog YAMLs, registry.yaml, the `docker mcp` CLI — works identically between macOS and Linux once the above pieces are in place.

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Running Docker MCP Gateway on Linux (Without Docker Desktop)