GRITS

Genetic Recombination Imputation Tool Set

Prerequisites

• pixi (v0.5+)
• NVIDIA-based GPU hardware with CUDA (v12+)
  • For gpu environment only (see next section)
• Linux or macOS OS environment preferred

Setup

Retrieve project code

git clone https://github.com/maize-genetics/grits.git
cd grits

Option A (preferred) - set up virtual environment (pixi)

# For CPU only
pixi install

# For Linux + GPU machines
pixi install --environment gpu

Option B - set up virtual environment (conda)

conda env create -f environment.yml

Run (CLI tool)

Conda:

python impute.py --input <input_file> --output <output_file> --model <imputation_method>

Pixi:

pixi run -- python impute.py --input <input_file> --output <output_file> --model <imputation_method>

Development (GUI app - experimental)

Prerequisites

• Node.js
• Rust (with wasm32-unknown-unknown target for web builds)
• wasm-pack (for web builds only)

Tauri Desktop App

If running this for the first time:

# First install pixi
# Next, run the pixi install script
pixi install

# Initialize npm environment
npm install

# Set up wheelhouse
npm run download-python
npm run build-wheelhouse

# Run the dev container of the Tauri app
npm run tauri dev

For subsequent runs, just use npm run tauri dev.

Static Web App (PS4G / BED Visualization)

The PS4G and BED visualization components can be built as a standalone static web application. File parsing runs entirely client-side via Rust compiled to WebAssembly -- no server required.

One-time setup

# Add the WASM compilation target
rustup target add wasm32-unknown-unknown

# Install wasm-pack
cargo install wasm-pack

# Install npm dependencies
npm install

Development

# Start the Vite dev server in web mode (port 3001)
npm run dev:web

Production build

# Build WASM + TypeScript + Vite to dist-web/
npm run build:web

# Preview the production build locally
npm run preview:web

The dist-web/ directory is a fully static site that can be deployed to GitHub Pages, Netlify, Vercel, S3, or any static file host.

Build commands reference

Command	Description
npm run dev	Vite dev server for Tauri (port 3000)
npm run dev:web	Vite dev server for web (port 3001)
npm run build	Production frontend build for Tauri (dist/)
npm run build:web	Full web pipeline: WASM + TS + Vite (dist-web/)
npm run build:wasm	Build only the WASM module (src/wasm/pkg/)
npm run preview:web	Serve the dist-web/ production build locally
npm run tauri dev	Launch the full Tauri desktop app in development mode

Testing

Run python unit tests with HTML output (CLI)

pytest --cov=src --cov-report=term-missing --cov-report=html