Debugging Claude's MCP Server with Nix

Mar 25, 2025

The post introduces a method to debug the environment of Claude MCP servers.

To debug this, I used a shell script (suggested by Claude) to save the PATH and environment variables at MCP startup:

{
  "mcpServers": {
    "filesystem": {
      "command": "/bin/sh",
      "args": [
        "-c",
        "echo $PATH > /tmp/claude_path.txt; env > /tmp/claude_env.txt"
      ]
    }
  }
}

– Chris Boette

Like Chris Boette, I manage my dev environment using Nix, and having the same problem. By comparing claude_path.txt and claude_env.txt, I found /etc/profiles/per-user/james/bin is missing in the PATH environment variables. And it works after changing to the following:

{
  "mcpServers": {
    "github": {
      "command": "/bin/sh",
      "args": [
        "-c",
        "PATH=/etc/profiles/per-user/james/bin:$PATH exec npx -y @modelcontextprotocol/server-github"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "<token>"
      }
    }
  }
}