The following is not necessary to run if you are following along with the tutorial. Only run these commands if you are publishing a new version or release of this document!
conda env create -n protocols --file qiime2-$RELEASE-py36-$ARCH-conda.yml
conda activate protocols
conda install -c conda-forge songbird redbiom -y
conda install -c bioconda bowtie2 -y
pip install https://github.com/knights-lab/SHOGUN/archive/v1.0.7.zip
pip install https://github.com/qiime2/q2-shogun/archive/master.zip
conda install cytoolz -y
conda install -c conda-forge sphinx awscli -y
export AWS_ACCESS_KEY_ID='MY_KEY_ID'
export AWS_SECRET_ACCESS_KEY='MY_SECRET_ACCESS_KEY'
make html
# once you have spot-checked the resulting HTML deploy the build:
make deploy
# and commit/push the latest `docs/` dir changes to this repo
git add docs/*
git commit -m "Some clever message here"
git push origin master