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.
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.
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Install the most recent development version of QIIME 2.
- 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
- 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
- macOS
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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
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Install additional dependencies:
pip install -r book/requirements.txt
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Build the book and initiate http server to host the book content:
make
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Open
http://localhost:8000
in your web browser. -
Read and enjoy. ๐ โ
docker pull github/super-linter:latest
docker run -e RUN_LOCAL=true -e VALIDATE_JSCPD=false -v $PWD:/tmp/lint github/super-linter