Snakemake Executor Tutorials

This set of tutorials are intended to introduce you to executing cloud executors. We start with the original Snakemake tutorial and expand upon it to be run in different cloud environments. For each run, we show you how to:

• authenticate with credentials, if required
• prepare your workspace
• submit a basic job
• generate an error and debug

The examples presented in these tutorials come from Bioinformatics. However, Snakemake is a general-purpose workflow management system for any discipline. We ensured that no bioinformatics knowledge is needed to understand the tutorial.

• Google Life Sciences Tutorial
  • Setup
  • Credentials
  • Step 1: Upload Your Data
  • Step 2: Write your Snakefile, Environment File, and Scripts
  • Step 3: Run Snakemake
  • Step 4: View Results
  • Step 5: Debugging
  • Step 6: Adding a Log File
• Auto-scaling Azure Kubernetes cluster without shared filesystem
  • Setup
  • Create an Azure storage account and upload data
  • Create an auto-scaling Kubernetes cluster
  • Running the workflow