polars-bio

(β˜… 192)

Blazing-Fast Bioinformatic Operations on Python DataFrames

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  • .gitignore
  • .pre-commit-config.yaml
  • .readthedocs.yaml
  • AGENTS.md
  • Cargo.lock
  • Cargo.toml
  • CHANGELOG.md
  • CLAUDE.md
  • CODE_OF_CONDUCT.md
  • HANDOVER-pgen-benchmarks.md
  • HANDOVER-pgen-perf.md
  • LICENSE
  • Makefile
  • mkdocs.yml
  • polars-bio.iml
  • pyproject.toml
  • README.md
  • requirements.txt
  • rust-toolchain.toml
  • rustfmt.toml
  • uv.lock

# Installation Guide

1. Get the code
git clone https://github.com/biodatageeks/polars-bio

Downloads the entire project code from GitHub to your computer.

cd polars-bio

Moves into the project folder you just downloaded.

2. Docker

Easy Recommended
Prerequisites
  • Git Needed to download the project code from GitHub.
  • Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
docker compose -f it/docker-compose.yml up -d --build

Runs the command against the services defined in the compose file.

βœ… Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.

3. Python

Easy
Prerequisites
  • Git Needed to download the project code from GitHub.
  • Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.
pip install -r requirements.txt

Installs the Python libraries listed in requirements.txt (or similar).

jupyter notebook

Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.

βœ… If it runs without errors and prints output in the terminal, it worked.

4. Rust

Medium
Prerequisites
  • Git Needed to download the project code from GitHub.
  • Rust (rustup) Installing via rustup also installs cargo.
cargo build --release

Compiles the Rust project.

cargo run

Builds and then immediately runs the program.

βœ… If cargo build finishes without errors, it worked. The executable is created under target/.

5. Make

Medium
Prerequisites
  • Git Needed to download the project code from GitHub.
  • Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).
make

Compiles the code based on the generated build configuration to produce an executable.

βœ… If it finishes without errors, it worked. Try running the generated executable directly.

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