cyverse/irods-mcp-server

iRODS MCP Server

The iRODS MCP Server provides access to data in iRODS. This project contains only the public, iRODS-related portions of the code for the AI Verde Data Store MCP Server.

Execution Modes

The iRODS MCP Server can run on an MCP Client machine using Docker in STDIO mode.

The iRODS MCP Server can also run on a dedicated server for multiple client users. In this case, the server supports both HTTP/SSE and Streamable-HTTP.

Run in an MCP Client Machine with Docker (with Claude Desktop)

Edit the ~/.config/Claude/claude_desktop_config.json file.

After editing, restart Claude Desktop to apply the changes.

a. Using Anonymous Access

This configuration allows access only to public data located at /iplant/home/shared.

{
    "mcpServers": {
        "irods": {
            "command": "docker",
            "args": [
                "run",
                "-i",
                "--rm",
                "-e",
                "IRODS_MCP_SVR_IRODS_SHARED_DIR_NAME=shared",
                "-e",
                "IRODS_HOST=data.cyverse.org",
                "-e",
                "IRODS_PORT=1247",
                "-e",
                "IRODS_ZONE_NAME=iplant",
                "cyverse/irods-mcp-server"
            ]
        }
    }
}

b. Using iRODS Account

This configuration allows access to your iRODS home directory (/<zone>/home/<username>) plus public data. Replace irods_username and irods_password with your actual credentials.

{
    "mcpServers": {
        "irods": {
            "command": "docker",
            "args": [
                "run",
                "-i",
                "--rm",
                "-e",
                "IRODS_MCP_SVR_IRODS_SHARED_DIR_NAME=shared",
                "-e",
                "IRODS_HOST=data.cyverse.org",
                "-e",
                "IRODS_PORT=1247",
                "-e",
                "IRODS_ZONE_NAME=iplant",
                "-e",
                "IRODS_USER_NAME=irods_username",
                "-e",
                "IRODS_USER_PASSWORD=irods_password",
                "cyverse/irods-mcp-server"
            ]
        }
    }
}

Run as a Server

Create a file named config.yaml and add the following:

remote: true
service_url: http://:8080
background: false
debug: true
log_path: ./irods-mcp-server.log

irods_host: data.cyverse.org
irods_port: 1247
irods_zone_name: iplant
irods_user_name: anonymous
irods_user_password: 

irods_proxy_auth: false
irods_shared_dir_name: shared
irods_webdav_url: https://data.cyverse.org/dav/

With this configuration, the server:

• Listens for incoming connections on port 8080
• Supports both HTTP/SSE and Streamable-HTTP requests
• Saves all logs (including debug info) to a file named irods-mcp-server.log
• Connects to iRODS host data.cyverse.org and port 1247
• Uses anonymous access by default
• Does not allow proxy auth
• Uses iplant as zone name and /iplant/home/shared as a public shared folder
• Uses https://data.cyverse.org/dav/ as a root in WebDAV URL generation for file access

Run the iRODS MCP Server executable using the command:

irods-mcp-server -c config.yaml

Once started, the server provides two endpoints:

• Endpoint URL for HTTP/SSE: http://localhost:8080/sse
• Endpoint URL for Streamable-HTTP service: http://localhost:8080/mcp

a. Setup VS Code for Anonymous Access

Edit the ~/.config/Code/User/mcp.json file.

This configuration allows access only to public data located at /<zone>/home/shared or /<zone>/home/public.

Replace the URL http://localhost:8080/mcp with the actual one where you are running the iRODS MCP Server.

{
    "servers": {
        "irods": {
            "type": "http",
            "url": "http://localhost:8080/mcp"
        }
    }
}

a. Setup VS Code for iRODS Account

Create a key from your iRODS account.

Use your CyVerse username (e.g., foo) and password (e.g., mypassword) separated by a colon (:) in the command below:

echo -n "foo:mypassword" | base64

The created key will be displayed in the Terminal.

Edit the ~/.config/Code/User/mcp.json file.

This configuration allows access to your iRODS home directory (/<zone>/home/<username>) plus public data.

Replace the URL http://localhost:8080/mcp with the actual one where you are running the iRODS MCP Server.

Replace the key YOUR_BASE64_KEY with the actual one created from your iRODS credentials. Your key must come after Basic (including the space).

{
    "servers": {
        "irods": {
            "type": "http",
            "url": "http://localhost:8080/mcp",
            "headers": {
				"Authorization": "Basic YOUR_BASE64_KEY"
			}
        }
    }
}