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[GH-ISSUE #3965] [BUG]: env key for mcp server not being used in windows #2522

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opened 2026-02-22 18:30:03 -05:00 by yindo · 1 comment
yindo commented 2026-02-22 18:30:03 -05:00
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Originally created by @tylerclendenin on GitHub (Jun 6, 2025).
Original GitHub issue: https://github.com/Mintplex-Labs/anything-llm/issues/3965

How are you running AnythingLLM?

AnythingLLM desktop app

What happened?

I am trying to use the following local MCP server and followed the instructions to install it

https://github.com/cyanheads/atlas-mcp-server

I have the following anythingllm_mcp_servers.json

{
  "mcpServers": {
    "atlas-mcp-server-stdio": {
      "command": "C:\\nvm4w\\nodejs\\node.exe",
      "args": ["C:\\Users\\tyler\\Documents\\Projects\\atlas-mcp-server\\dist\\index.js"],
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USER": "neo4j",
        "NEO4J_PASSWORD": "password2",
        "MCP_LOG_LEVEL": "info",
        "NODE_ENV": "development",
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

I added some debug code to the built js to log the environment and the env keys I passed in do not show up.

Additionally, I tried using a .env file in the project root, however the cwd ended up being my user folder, and it did not change if I added a "cwd" key to the server's json. (That might be a separate feature request, and I do not know if there is a standard, but this might be a good reference https://gist.github.com/timheuer/7b092645f01fe15fad2a96677d0b34e6)

Are there known steps to reproduce?

I was not able to get env variables to work when I created any mcp server on windows 11 with a user installation or AnythingLLM desktop

Originally created by @tylerclendenin on GitHub (Jun 6, 2025). Original GitHub issue: https://github.com/Mintplex-Labs/anything-llm/issues/3965 ### How are you running AnythingLLM? AnythingLLM desktop app ### What happened? I am trying to use the following local MCP server and followed the instructions to install it https://github.com/cyanheads/atlas-mcp-server I have the following anythingllm_mcp_servers.json ``` { "mcpServers": { "atlas-mcp-server-stdio": { "command": "C:\\nvm4w\\nodejs\\node.exe", "args": ["C:\\Users\\tyler\\Documents\\Projects\\atlas-mcp-server\\dist\\index.js"], "env": { "NEO4J_URI": "bolt://localhost:7687", "NEO4J_USER": "neo4j", "NEO4J_PASSWORD": "password2", "MCP_LOG_LEVEL": "info", "NODE_ENV": "development", "MCP_TRANSPORT_TYPE": "stdio" } } } } ``` I added some debug code to the built js to log the environment and the env keys I passed in do not show up. Additionally, I tried using a .env file in the project root, however the cwd ended up being my user folder, and it did not change if I added a "cwd" key to the server's json. (That might be a separate feature request, and I do not know if there is a standard, but this might be a good reference https://gist.github.com/timheuer/7b092645f01fe15fad2a96677d0b34e6) ### Are there known steps to reproduce? I was not able to get env variables to work when I created any mcp server on windows 11 with a user installation or AnythingLLM desktop
yindo added the possible bug label 2026-02-22 18:30:03 -05:00
yindo closed this issue 2026-02-22 18:30:03 -05:00
yindo commented 2026-02-22 18:30:03 -05:00
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@timothycarambat commented on GitHub (Jun 6, 2025):

Fixed in https://github.com/Mintplex-Labs/anything-llm/pull/3909 and will be in next desktop update

@timothycarambat commented on GitHub (Jun 6, 2025): Fixed in https://github.com/Mintplex-Labs/anything-llm/pull/3909 and will be in next desktop update
yindo changed title from [BUG]: env key for mcp server not being used in windows to [GH-ISSUE #3965] [BUG]: env key for mcp server not being used in windows 2026-06-05 14:47:02 -04:00
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Reference: Mintplex-Labs/anything-llm#2522
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