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QIIME 2 Cancer Microbiome Intervention Tutorial

This repository contains the source for the QIIME 2 Cancer Microbiome Intervention Tutorial. This content is presented as a Jupyter Book here.

You shouldn't need to access this source repository if you're interested in following the tutorial or reading other parts of the Jupyter Book.

About QIIME 2 Usage API enabled Jupyter Books

QIIME 2 Usage API enabled Jupyter Books allow for the development of Jupyter Books that can illustrate QIIME 2 workflows as steps in different QIIME 2 interfaces.

For developers and tutorial authors

Building this Jupyter Book

  1. Install the most recent development version of QIIME 2.

    1. macOS 
      wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda env create -n q2-jb --file qiime2-amplicon-macos-latest-conda.yml
conda activate q2-jb
    2. Linux 
      wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
conda env create -n q2-jb --file qiime2-amplicon-ubuntu-latest-conda.yml
conda activate q2-jb

  2. Obtain Jupyter Book content by cloning this repository and changing into the new directory that is created:

    git clone git@github.com:qiime2/cancer-microbiome-intervention-tutorial.git
cd cancer-microbiome-intervention-tutorial

  3. Install additional dependencies:

    pip install -r book/requirements.txt

  4. Build the book and initiate http server to host the book content:

    make

  5. Open http://localhost:8000 in your web browser.

  6. Read and enjoy. 📚 ☕

Local Linting

docker pull github/super-linter:latest
docker run -e RUN_LOCAL=true -e VALIDATE_JSCPD=false -v $PWD:/tmp/lint github/super-linter