Convert To Docker

Convert to Docker

This skill migrates BioClaw from Apple Container (macOS-only) to Docker for cross-platform support (macOS and Linux).

What this changes:

• Container runtime: Apple Container → Docker
• Mount syntax: --mount type=bind,...,readonly → -v path:path:ro
• Startup check: container system status → docker info
• Build commands: container build/run → docker build/run

What stays the same:

• Dockerfile (already Docker-compatible)
• Agent runner code
• Mount security/allowlist validation
• All other functionality

Prerequisites

Verify Docker is installed before starting:

docker --version && docker info >/dev/null 2>&1 && echo "Docker ready" || echo "Install Docker first"

If Docker is not installed:

• macOS: Download from https://docker.com/products/docker-desktop
• Linux: curl -fsSL https://get.docker.com | sh && sudo systemctl start docker

1. Update Container Runner

Edit src/container-runner.ts:

1a. Update module comment (around line 3)

// Before:
 * Spawns agent execution in Apple Container and handles IPC

// After:
 * Spawns agent execution in Docker container and handles IPC

1b. Update directory mount comment (around line 88)

// Before:
    // Apple Container only supports directory mounts, not file mounts

// After:
    // Docker bind mounts work with both files and directories

1c. Update env workaround comment (around line 120)

// Before:
  // Environment file directory (workaround for Apple Container -i env var bug)

// After:
  // Environment file directory (keeps credentials out of process listings)

1d. Update buildContainerArgs function

Replace the entire function with Docker mount syntax:

function buildContainerArgs(mounts: VolumeMount[]): string[] {
  const args: string[] = ['run', '-i', '--rm'];

  // Docker: -v with :ro suffix for readonly
  for (const mount of mounts) {
    if (mount.readonly) {
      args.push('-v', `${mount.hostPath}:${mount.containerPath}:ro`);
    } else {
      args.push('-v', `${mount.hostPath}:${mount.containerPath}`);
    }
  }

  args.push(CONTAINER_IMAGE);

  return args;
}

1e. Update spawn command (around line 204)

// Before:
    const container = spawn('container', containerArgs, {

// After:
    const container = spawn('docker', containerArgs, {

2. Update Startup Check

Edit src/index.ts:

2a. Replace the container system check function

Find ensureContainerSystemRunning() and replace entirely with:

function ensureDockerRunning(): void {
  try {
    execSync('docker info', { stdio: 'pipe', timeout: 10000 });
    logger.debug('Docker daemon is running');
  } catch {
    logger.error('Docker daemon is not running');
    console.error('\n╔════════════════════════════════════════════════════════════════╗');
    console.error('║  FATAL: Docker is not running                                  ║');
    console.error('║                                                                ║');
    console.error('║  Agents cannot run without Docker. To fix:                     ║');
    console.error('║  macOS: Start Docker Desktop                                   ║');
    console.error('║  Linux: sudo systemctl start docker                            ║');
    console.error('║                                                                ║');
    console.error('║  Install from: https://docker.com/products/docker-desktop      ║');
    console.error('╚════════════════════════════════════════════════════════════════╝\n');
    throw new Error('Docker is required but not running');
  }
}

2b. Update the function call in main()

// Before:
  ensureContainerSystemRunning();

// After:
  ensureDockerRunning();

3. Update Build Script

Edit container/build.sh:

3a. Update build command (around line 15-16)

# Before:
# Build with Apple Container
container build -t "${IMAGE_NAME}:${TAG}" .

# After:
# Build with Docker
docker build -t "${IMAGE_NAME}:${TAG}" .

3b. Update test command (around line 23)

# Before:
echo "  echo '{...}' | container run -i ${IMAGE_NAME}:${TAG}"

# After:
echo "  echo '{...}' | docker run -i ${IMAGE_NAME}:${TAG}"

4. Update Documentation

Update references in documentation files:

Key README.md updates:

Requirements section:

## Requirements

- macOS or Linux
- Node.js 20+
- [Claude Code](https://claude.ai/download)
- [Docker](https://docker.com/products/docker-desktop)

FAQ - "Why Docker?":

**Why Docker?**

Docker provides cross-platform support (macOS and Linux), a large ecosystem, and mature tooling. Docker Desktop on macOS uses a lightweight Linux VM similar to other container solutions.

FAQ - "Can I run this on Linux?":

**Can I run this on Linux?**

Yes. BioClaw uses Docker, which works on both macOS and Linux. Just install Docker and run `/setup`.

5. Update Skills

5a. Update .claude/skills/setup/SKILL.md

Replace Section 2 "Install Apple Container" with Docker installation:

## 2. Install Docker

Check if Docker is installed and running:

\`\`\`bash
docker --version && docker info >/dev/null 2>&1 && echo "Docker is running" || echo "Docker not running or not installed"
\`\`\`

If not installed or not running, tell the user:
> Docker is required for running agents in isolated environments.
>
> **macOS:**
> 1. Download Docker Desktop from https://docker.com/products/docker-desktop
> 2. Install and start Docker Desktop
> 3. Wait for the whale icon in the menu bar to stop animating
>
> **Linux:**
> \`\`\`bash
> curl -fsSL https://get.docker.com | sh
> sudo systemctl start docker
> sudo usermod -aG docker $USER  # Then log out and back in
> \`\`\`
>
> Let me know when you've completed these steps.

Wait for user confirmation, then verify:

\`\`\`bash
docker run --rm hello-world
\`\`\`

Update build verification:

Verify the build succeeded:

\`\`\`bash
docker images | grep bioclaw-agent
echo '{}' | docker run -i --entrypoint /bin/echo bioclaw-agent:latest "Container OK" || echo "Container build failed"
\`\`\`

Update troubleshooting section to reference Docker commands.

5b. Update .claude/skills/debug/SKILL.md

Replace all container commands with docker equivalents:

Update the architecture diagram header:

Host (macOS/Linux)                    Container (Docker)

6. Build and Verify

After making all changes:

# Compile TypeScript
npm run build

# Build Docker image
./container/build.sh

# Verify image exists
docker images | grep bioclaw-agent

7. Test the Migration

7a. Test basic container execution

echo '{}' | docker run -i --entrypoint /bin/echo bioclaw-agent:latest "Container OK"

7b. Test readonly mounts

mkdir -p /tmp/test-ro && echo "test" > /tmp/test-ro/file.txt
docker run --rm --entrypoint /bin/bash -v /tmp/test-ro:/test:ro bioclaw-agent:latest \
  -c "cat /test/file.txt && touch /test/new.txt 2>&1 || echo 'Write blocked (expected)'"
rm -rf /tmp/test-ro

Expected: Read succeeds, write fails with "Read-only file system".

7c. Test read-write mounts

mkdir -p /tmp/test-rw
docker run --rm --entrypoint /bin/bash -v /tmp/test-rw:/test bioclaw-agent:latest \
  -c "echo 'test write' > /test/new.txt && cat /test/new.txt"
cat /tmp/test-rw/new.txt && rm -rf /tmp/test-rw

Expected: Both operations succeed.

7d. Full integration test

npm run dev
# Send @AssistantName hello via WhatsApp
# Verify response received

Troubleshooting

Docker not running:

• macOS: Start Docker Desktop from Applications
• Linux: sudo systemctl start docker
• Verify: docker info

Permission denied on Docker socket (Linux):

sudo usermod -aG docker $USER
# Log out and back in

Image build fails:

# Clean rebuild
docker builder prune -af
./container/build.sh

Container can't write to mounted directories: Check directory permissions on the host. The container runs as uid 1000.

Summary of Changed Files