Automate away friction

Automation tools

snakemake

There are many good online tutorials on using different automation tools, to mention a few, CodeRefinery has arranged snakemake hackathons and tutorials.

Research Software hour 005: Interview with Sarah Gibson, Snakemake, workflow automation intro, etc.

Containers

podman is a great open source (and docker alternative) way of building, managing, and running containers. There is a nice short tutorial blog on redhat detailing how to make your own first container. If you want to play around with podman you can install it and have a look at the Containerfile specification.

Building

Generic

• Meson Build
• GNU Make
• waf
• SCons
• EasyBuild

Python

• setuptools
• hatch
• filt
• pdm

Installing

• python installer
• arch packages
• ubuntu packages

ansible

Ansible is a powerful open source automation tool that allows you to execute tasks on a set of systems, be it local or remote. I have been using to manage the many computers involved in the meteor camera network as well as for keeping my virtual machines up to date.

CI

• GitLab CI
• Github Actions
• Jenkins
• Ambient

Environments and packages

• Lmod
• pixi

Why automation

A while back I read this blog post about a company that owned about 400 million dollars in assets went bankrupt in about 45 minutes because of an error in a manual deployment. It is an interesting story that I would recommend looking into. If you would rather watch than read, there is of course a reaction video about the incident!

Bankrupt In 45 Minutes From DevOps | Prime Reacts

Homework assignments

This task is simply to identify some workflow you have, whatever that may be, that would benefit from automation, and then to automate it!