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Installing byok8s

byok8s requires pieces of prerequisite software:

  • python (conda)
  • virtualenv (optional)

Additionally, if you are planning to run byok8s on a local virtual kubernetes cluster, you must install:

  • minikube

Otherwise, if you are planning on running byok8s on remote kubernetes clusters provided by cloud providers or etc., you must install:

  • kubernetes, OR
  • a cloud provider command line tool (gcloud, aws)

Installing Python

We recommend installing pyenv and using pyenv to install miniconda:

curl | bash

Restart your shell and install miniconda:

pyenv update
pyenv install miniconda3-4.3.30
pyenv global miniconda3-4.3.30

Installing virtualenv

You will need the virtualenv package to set up a virtual environment:

pip install virtualenv

Installing minikube

This step is only required if you plan to run byok8s kubernetes workflows locally on a virtual kubernetes cluster (i.e., testing mode).

Install the 64-bit Linux version of minikube, or visit the installing minikube to find the right version:

curl -LO \
  && sudo install minikube-linux-amd64 /usr/local/bin/minikube

(On a Mac you can do brew install minikube.)

If you are planning on running on a bare metal machine, you will also need to install a hypervisor like VirtualBox or KVM, see installing minikube.

If you are planning on running minikube on a compute node in the cloud, you cannot run a hypervisor, so you will need to run using the native driver; see installing minikube.

Once you have installed minikube, you do not need to install kubernetes.

Installing byok8s

Start by cloning the repo and installing byok8s:

git clone
cd ~/2019-snakemake-byok8s

Next, you'll create a virtual environment:

virtualenv vp
source vp/bin/activate

pip install -r requirements.txt
python build install

Now you should be ready to rock:

which byok8s

This will only be present when you have activated your virtual environment. To activate/re-activate your virtual environment:

cd ~/2019-snakemake-byok8s
source vp/bin/activate