Unable to select multiple toolsets using docker run

[tadasant]

Describe the bug

This command from the README does not work for me:

$ docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN=ghp_... -e GITHUB_TOOLSETS="repos,issues,pull_requests,code_security,experiments" ghcr.io/github/github-mcp-server
2025/05/12 17:03:08 Failed to initialize toolsets:toolset repos,issues,pull_requests,code_security,experiments does not exist

Nor does a slightly simpler one:

$ docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN=ghp_... -e GITHUB_TOOLSETS="repos,issues" ghcr.io/github/github-mcp-server
2025/05/12 17:00:52 Failed to initialize toolsets:toolset repos,issues does not exist

But these work fine:

$ docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN=ghp_... -e GITHUB_TOOLSETS="repos" ghcr.io/github/github-mcp-server
GitHub MCP Server running on stdio

$ docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN=ghp_... -e GITHUB_TOOLSETS="all" ghcr.io/github/github-mcp-server
GitHub MCP Server running on stdio

Seems to be something related to parsing a comma-separated entry?

Affected version

Please run docker run -i --rm ghcr.io/github/github-mcp-server ./github-mcp-server --version and paste the output below

GitHub MCP Server
Version: v0.2.1
Commit: 9fa582d8d63522d70ce8f3af58265effb9645323
Build Date: 2025-04-21T23:03:01Z

[stefan-it]

I can confirm this, and I found a solution in this issue:

#307 (comment)

Which is working for me :)

[tadasant]

Oops, thank you! Missed the Closed issue :)

Sadly the workaround doesn't work for me, because Cursor seems to automatically turn that ./github-mcp-server path to an absolute:

2025-05-12 14:08:38.348 [info] thub: Starting new stdio process with command: docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN=ghp_... ghcr.io/github/github-mcp-server /Users/admin/github-projects/mcp-servers/github-mcp-server stdio --toolsets repos,issues

From this config:

    "github": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e",
        "GITHUB_PERSONAL_ACCESS_TOKEN=ghp_...
        "ghcr.io/github/github-mcp-server",
        "./github-mcp-server",
        "stdio",
        "--toolsets",
        "repos,issues"
      ]
    },

But regardless the main issue here sounds like it's fixed just unreleased, so I'll close.