tools

This repository documents a collection of data science and computer science tools, including their core concepts, command-line usage, and representative outputs. It also provides runnable environments for hands-on experimentation, and a GitHub Pages–hosted website for quick reference and command lookup:

👉 https://benson1231.github.io/tools/

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Repository Structure and Design Philosophy

This repository adopts a decoupled architecture that clearly separates computation, artifacts, and presentation.

• website/docs/ Contains Quarto (.qmd) files used for documentation, tutorials, and methodological explanations.

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Clone This Repository

To run the tools locally, clone this repository:

git clone https://github.com/benson1231/tools.git
cd tools
mkdir results/

Please refer to the environment documentation in envs/README.md to set up a runnable environment.

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Render the Website

To build the website locally, install Quarto or create a ready-to-use environment using envs/quarto.yaml.

quarto render ./website

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If you want run the codes in your machine

See envs/ folder

mamba env create -f envs/ENV-YAML-FILE -y
mamba activate ENV-NAME

example:

mamba env create -f envs/ngs-tools.yaml -y
mamba activate ngs-tools

退出與刪除環境

# exit conda environment
mamba deactivate

# remove conda environment (replace `ENV-NAME` to your environment name)
mamba env remove -n ENV-NAME -y