Repository with code to provision an AKS cluster which can be used to dynamically scale compute resources for an arbitrary Snakemake pipeline.
This repo uses conda to simplify dependency management and installation. To get started with setup you can install miniconda3 using the instructions available here: https://docs.conda.io/en/latest/miniconda.html.
The first step to deploying an analysis pipeline is to install the various software packages it depends on.
All commands should be executed from the top level directory of this repository.
Conda can be used to install all Python and most OS system dependencies using:
conda env create --file envs/aks-snakemake.yml
This will take some time to run as it gathers and installs the correct package versions. The environment it creates should be called aks-snakemake.
If it is not automatically activated after installation please run
conda activate aks-snakemake before proceeding to the next step.
Open the files named dot_*, fill in your values for the requested configuration variables, then rename the files as instructed in the
comments in each file.
This will ensure your specific configuration is not pushed to the GitHub.
TODO::