### Install Dependencies and Setup

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/developer-guides/02-contributing-and-testing.md

Install project dependencies and set up the development environment. The 'make install' command is recommended for a complete setup.

```bash
# Recommended: Use make for complete setup
make install
```

```bash
# Alternative: Manual setup
uv sync --all-extras
uv run pre-commit install
```

--------------------------------

### Usage Example for xresources Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Use this example to manage X resources configuration in your home setup. To see all available options, execute `home_manager_options_by_prefix("xresources")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  xresources.<option> = <value>;
}
```

--------------------------------

### Quick Start BioMCP Client Usage

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/apis/python-sdk.md

A quick start example demonstrating how to initialize the BioMCP client and perform common searches for articles, trials, and variants.

```python
import asyncio
from biomcp import BioMCPClient

async def main():
    async with BioMCPClient() as client:
        # Search articles
        articles = await client.articles.search(
            genes=["BRAF"],
            diseases=["melanoma"],
            limit=5
        )

        # Get trial details
        trial = await client.trials.get("NCT03006926")

        # Search variants
        variants = await client.variants.search(
            gene="TP53",
            significance="pathogenic"
        )

asyncio.run(main())
```

--------------------------------

### Usage Example for nixpkgs Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

This example demonstrates how to set nixpkgs-related options within your home configuration. For a complete list, consult `home_manager_options_by_prefix("nixpkgs")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  nixpkgs.<option> = <value>;
}
```

--------------------------------

### Usage Example for pam Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Configure Pluggable Authentication Modules (PAM) settings with this example in your home configuration. For a comprehensive list, run `home_manager_options_by_prefix("pam")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  pam.<option> = <value>;
}
```

--------------------------------

### Usage Example for fonts Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Configure font-related settings using this example in your home configuration. Use `home_manager_options_by_prefix("fonts")` to discover all available font options.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  fonts.<option> = <value>;
}
```

--------------------------------

### Usage Example for lib Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

This snippet shows how to configure options within the 'lib' category in your home configuration. Use `home_manager_options_by_prefix("lib")` to view all available options.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  lib.<option> = <value>;
}
```

--------------------------------

### Example Nix-Darwin Homebrew Enable Configuration

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Example showing how to set the `homebrew.enable` option to true in Nix-Darwin configuration. This enables Homebrew management.

```nix
true
```

--------------------------------

### Example Use Case: Travel Planning

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/weather_mcp/weather-mcp/README.md

Demonstrates how to call the `get_weather_forecast_tool` to get a week's weather forecast for travel planning.

```python
get_weather_forecast_tool(city="Paris", days=7)
```

--------------------------------

### Home Manager Git Configuration Example

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

An example Nix configuration for enabling and customizing Git using Home Manager. This includes setting user name, email, and enabling features like diff-so-fancy.

```nix
{
  programs.git = {
    enable = true
    userName = "John Doe"
    userEmail = "john.doe@example.com"
    diffSoFancy.enable = true
  };
}
```

--------------------------------

### Usage Example for editorconfig Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

This example shows how to configure EditorConfig settings in your home configuration. To list all available options, use `home_manager_options_by_prefix("editorconfig")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  editorconfig.<option> = <value>;
}
```

--------------------------------

### Usage Example for manual Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Use this snippet to configure manual-related options in your home configuration. Refer to `home_manager_options_by_prefix("manual")` for a full list of available options.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  manual.<option> = <value>;
}
```

--------------------------------

### Usage Example for dconf Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Configure dconf settings in your home configuration using this pattern. For a complete list of options, run `home_manager_options_by_prefix("dconf")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  dconf.<option> = <value>;
}
```

--------------------------------

### Search Nix-Darwin Options for 'brew'

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Searches Nix-Darwin options for a given query, returning relevant configuration paths and descriptions. This example searches for 'brew'.

```nix
{ `limit`: 5, `query`: `brew` }
```

--------------------------------

### Install Node.js on Windows

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/troubleshooting.md

Instructions for installing Node.js on Windows. Download the installer from the official Node.js website.

```powershell
# Install Node.js from https://nodejs.org
```

--------------------------------

### Install Development Dependencies

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/wikipedia-mcp/CONTRIBUTING.md

Install the project's development dependencies, including editable installs.

```bash
pip install -e ".[dev]"
```

--------------------------------

### Usage Example for news Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Configure news feed settings in your home configuration with this snippet. Find all news-related options by running `home_manager_options_by_prefix("news")`.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  news.<option> = <value>;
}
```

--------------------------------

### Install AlphaGenome

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/tutorials/claude-code-biomcp-alphagenome.md

Clones the AlphaGenome repository and installs it using uv.

```bash
git clone https://github.com/google-deepmind/alphagenome.git
cd alphagenome && uv pip install .
```

--------------------------------

### Home Manager Option Statistics

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Example output showing Home Manager option statistics.

```text
# Home Manager Option Statistics
Total options: 3704
Categories: 4
Option types: 391
## Distribution by Source
- options: 3697 options
- nix-darwin-options: 7 options
## Top Categories
- Note: 1943 options
- Caution: 1264 options
- Uncategorized: 430 options
- Warning: 74 options
## Distribution by Type
- boolean: 936 options
- null or string: 300 options
- string: 282 options
- package: 239 options
- list of string: 175 options
- strings concatenated with “\n”: 145 options
- null or boolean: 137 options
- null or package: 136 options
- null or signed integer: 82 options
- attribute set of string: 71 options
## Index Statistics
- Words indexed: 4382
- Prefix paths: 4432
- Hierarchical parts: 4403
```

--------------------------------

### Usage Example for i18n Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Configure internationalization (i18n) settings in your home configuration using this pattern. See `home_manager_options_by_prefix("i18n")` for all available i18n options.

```nix
# In your home configuration (e.g., ~/.config/nixpkgs/home.nix)
{
  config,
  pkgs,
  ...
}: {
  i18n.<option> = <value>;
}
```

--------------------------------

### NixOS Search Query

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Example of a NixOS search query for programs.

```json
{
  `ctx`: `Checking NixOS search for programs`,
  `type`: `programs`,
  `limit`: 5,
  `query`: `git`
}
```

--------------------------------

### Home Manager Search Query

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Example of a Home Manager search query.

```json
{
  `ctx`: `Checking Home Manager search`,
  `limit`: 5,
  `query`: `neovim`
}
```

--------------------------------

### Add Nginx Echo Module

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Install additional third-party nginx modules. Packaged modules are available in `pkgs.nginxModules`.

```nix
[ pkgs.nginxModules.echo ]
```

```nix
# /etc/nixos/configuration.nix
{
  config,
  pkgs,
  ...
}: {
  services.nginx = {
    additionalModules = [ pkgs.nginxModules.echo ];
  };
}
```

--------------------------------

### NixOS Search Query for PostgreSQL Options

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/app/docs/claude.html

Example of how to use nixos_search to find all options related to the PostgreSQL service.

```json
{
  `ctx`: `Searching for all PostgreSQL options in NixOS`,
  `type`: `options`,
  `limit`: 50,
  `query`: `services.postgresql`
}
```

--------------------------------

### MCP Configuration for Wikipedia

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/wikipedia-mcp/PUBLISHING_GUIDE.md

Example JSON configuration for adding the wikipedia package to an MCP server setup. Specifies the command and arguments for installation.

```json
{
  "wikipedia": {
    "command": "uvx",
    "args": ["wikipedia-mcp"]
  }
}
```

--------------------------------

### Cloudflare Worker Routing for MCP Endpoint

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/developer-guides/04-transport-protocol.md

Example of a Cloudflare Worker setup that handles both legacy SSE (GET) and Streamable HTTP (POST) requests on the /mcp endpoint.

```javascript
// Automatically routes based on method
.get("/mcp", async (c) => {
  // Legacy SSE transport
})
.post("/mcp", async (c) => {
  // Streamable HTTP transport
})
```

--------------------------------

### Get Specific Trial Details Example

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/backend-services-reference/05-nci-cts-api.md

Example cURL request to retrieve detailed information for a specific clinical trial using its NCT ID.

```bash
curl -X GET "https://clinicaltrialsapi.cancer.gov/api/v2/trials/NCT04280705" \
  -H "X-API-KEY: your-key"
```

--------------------------------

### Install Node.js on Linux

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/troubleshooting.md

Installs the latest LTS version of Node.js on Linux using NodeSource setup script and apt-get. This is necessary for using npx and other Node.js tools.

```bash
# Install Node.js
curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash -
sudo apt-get install -y nodejs
```

--------------------------------

### Date-Based Trial Search

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/how-to-guides/02-find-trials-with-nci-and-biothings.md

Find trials that started within a specific date range, useful for identifying recently initiated studies. This example filters for trials started in 2024.

```bash
# CLI - Trials started in 2024
biomcp trial search \
  --condition cancer \
  --start-date 2024-01-01 \
  --status RECRUITING
```

--------------------------------

### Manual Website Setup and Development Commands

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/mcp-nixos/website/README.md

These commands are used for setting up the website development environment and running tasks manually, without Nix.

```bash
# Navigate to the website directory
cd website

# Install dependencies
npm install
# or
yarn
# or
pnpm install

# Start development server
npm run dev
# or
yarn dev
# or
pnpm dev

# Build for production
npm run build
# or
yarn build
# or
pnpm build
```

--------------------------------

### Example JSON for Get Current Weather Tool

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/weather_mcp/weather-mcp/README.md

This JSON payload is used to invoke the `get_current_weather_tool`. It requires the 'city' parameter.

```json
{
  "city": "Istanbul"
}
```

--------------------------------

### Basic BioMCP Dockerfile

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/developer-guides/01-server-deployment.md

A Dockerfile to build a container image for BioMCP, including installation and environment variable setup for API keys.

```dockerfile
FROM python:3.11-slim

# Install BioMCP
RUN pip install biomcp-python

# Add API keys (use secrets in production!)
ENV NCI_API_KEY=""
ENV ALPHAGENOME_API_KEY=""

# Expose port
EXPOSE 8000

# Run server
CMD ["biomcp", "run", "--mode", "http", "--host", "0.0.0.0"]
```

--------------------------------

### MCP Server API - Get Current Weather Output

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/weather_mcp/README_MCP_WEATHER.md

Example output from the `get_current_weather_tool`, showing current weather details for a city.

```json
{
  "output": {
    "city": "Istanbul",
    "country": "Turkey",
    "temperature_c": 15.0,
    "weather": "Partly cloudy",
    "humidity": 65,
    "wind_kph": 10.8,
    "pressure_mb": 1013.0,
    "uv_index": 4
  }
}
```

--------------------------------

### MCP Server API - Get Current Weather Input

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/weather_mcp/README_MCP_WEATHER.md

Example input for the `get_current_weather_tool` to retrieve current weather data for a specified city.

```json
{
  "input": {
    "city": "Istanbul"
  }
}
```

--------------------------------

### Faceted Search Example

Source: https://github.com/accenture/mcp-bench/blob/main/mcp_servers/biomcp/docs/backend-services-reference/02-biothings-suite.md

Illustrates how to use faceted search to get aggregations and counts for specific fields, often used for filtering and analysis.

```APIDOC
## Advanced Feature: Faceted Search

### Description
Faceted search enables you to retrieve aggregations (counts) for specified fields based on your query. This is commonly used for building interactive filters or understanding data distribution.

### Get aggregations
```python
params = {
    "q": "clinvar.clinical_significance:pathogenic",
    "facets": "dbnsfp.genename",
    "size": 0  # Set size to 0 to only return facets and no actual hits
}
```
```