Build the container
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docker-based mcp server that enables Claude to fetch biological sequence data from NCBI
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- Author
- actual-awg
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Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
Build the containerCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Clone the repository, change into its directory, build the Docker image with docker build -t ncbi-mcp-server ., then run it with docker run -it --rm ncbi-mcp-server. For Claude Desktop, add the provided JSON configuration to claude_desktop_config.json.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"build the container": {
"ncbi-sequence-fetcher": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"ncbi-mcp-server"
]
}
}
}
}McpServers
{
"ncbi-sequence-fetcher": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"ncbi-mcp-server"
]
}
}to get this running you will need to clone the repository and cd into the directory, then run:
Build the container
docker build -t ncbi-mcp-server .
Run with stdio transport (for Claude Desktop)
docker run -it --rm ncbi-mcp-server
make sure you add this to claude_desktop_config.json ($env:AppData\Claude\claude_desktop_config.json on windows)
``
json{
"mcpServers": {
"ncbi-sequence-fetcher": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"ncbi-mcp-server"
]
}
}
}
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