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Troubleshooting ClojureMCP

This guide covers common issues when setting up ClojureMCP, particularly with Claude Desktop.

Quick Checklist

If Claude Desktop can't run the clojure command:

  1. Test your command manually: Run the exact command from your config in a terminal
  2. Check your PATH: Ensure which clojure works in a fresh terminal
  3. Enable logging: Check Claude Desktop logs for error messages
  4. Simplify first: Start with a basic configuration, then add complexity

If you continue to have issues, consider consulting with AI assistants (Claude, ChatGPT, Gemini) about the specific PATH configuration for your system setup.

PATH Issues (Most Common)

If your claude_desktop_config.json doesn't work, it's most likely that the PATH environment variable is not set up correctly to find clojure and java.

You can fix this by explicitly setting the PATH environment variable:

{
    "mcpServers": {
        "clojure-mcp": {
            "command": "/opt/homebrew/bin/bash",
            "args": [
                "-c",
                "export PATH=/opt/homebrew/bin:$PATH; exec clojure -Tmcp start :not-cwd true :port 7888"
            ]
        }
    }
}

Common PATH Locations

  • Homebrew (Apple Silicon): /opt/homebrew/bin
  • Homebrew (Intel Mac): /usr/local/bin
  • Nix: /home/username/.nix-profile/bin or /nix/var/nix/profiles/default/bin
  • System Default: /usr/bin:/usr/local/bin

Debugging Strategies

These are some examples to give you a way to debug a failed ClojureMCP startup.

Examine the environment

{
    "mcpServers": {
        "clojure-mcp": {
            "command": "/opt/homebrew/bin/bash",
            "args": [
                "-c",
                "echo $PATH > /Users/yourname/claude-desktop-path.txt"
            ]
        }
    }
}

Capture ClojureMCP output

{
    "mcpServers": {
        "clojure-mcp": {
            "command": "/opt/homebrew/bin/bash",
            "args": [
                "-c",
                "clojure -Tmcp start :not-cwd true :port 7888 | tee /Users/yourname/clojure-mcp-stdout.log"
            ]
        }
    }
}

Advanced Configuration Example

If you need to source environment variables (like API keys, see LLM API Keys):

{
    "mcpServers": {
        "clojure-mcp": {
            "command": "/bin/sh",
            "args": [
                "-c",
                "source ~/.my-llm-api-keys.sh && PATH=/Users/username/.nix-profile/bin:$PATH && clojure -Tmcp start :not-cwd true :port 7888"
            ]
        }
    }
}

Connection Refused Error

Execution error (ConnectException) at sun.nio.ch.Net/connect0 (Net.java:-2).
Connection refused

This means ClojureMCP couldn't connect to your nREPL server. Ensure:

  • The nREPL server is running
  • The port numbers match (default: 7888)

Extraneous Output

If you see output other than JSON-RPC messages, it's likely due to ClojureMCP being included in a larger environment. Ensure ClojureMCP runs with its own isolated dependencies.

Claude Desktop Logs

Claude Desktop logs can be found at:

  • macOS: ~/Library/Logs/Claude/
  • Windows: %APPDATA%\Claude\logs\

Check these logs for detailed error messages when ClojureMCP fails to start.