colinvwood / cancer-microbiome-intervention-tutorial

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/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml
      conda env create -n q2-jb --file qiime2-latest-py38-osx-conda.yml
      conda activate q2-jb
      

   2. Linux

      wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml
      conda env create -n q2-jb --file qiime2-latest-py38-linux-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 [email protected]: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