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Scientific Containers CRG PhD Course 2024

Reproducible research using Containers

About the course

This slow-paced hands-on course is designed for absolute beginners who want to start using Linux Containers (Docker and Singularity/Apptainer).

Outline

The course will train participants to run and build Linux containers.

It is designed to provide trainees with short and frequent hands-on sessions while keeping theoretical sessions to a minimum.

Learning objectives

  • Locate and fetch Docker/Singularity images from dedicated repositories.
  • Execute/Run a Docker/Singularity container from the command line.
  • Build simple Docker container images

Prerequisite / technical requirements

Being comfortable working with the CLI (command-line interface) in a Linux-based environment. The course materials are online on the dedicated GitHub page for self-learning.

Practitioners must connect to a remote server via the "ssh" protocol during the course. You can learn about it here.

Those who follow the course should be able to use a command-line/screen-oriented text editor (such as nano or vi/vim, already available on the server) or an editor that can connect remotely. For the sake of information, below are the basics of "nano": https://wiki.gentoo.org/wiki/Nano/Basics_Guide

Dates, time, location

  • Dates: 21th October 2024. Time: 12:00 - 17:00h (CET)

  • Location: Online

Program

  • 12:00-13:00 Introduction to containers and Docker/Podman
  • 13:00-14:00 Lunch Break
  • 14:00-16:00 Docker
  • 16:00-17:00 Singularity/Apptainer

Acknowledgements

  • Sphinx. The publication system for our course pages.
  • ELIXIR Workshop Hackathon. Joined initiative with other colleagues to exchange materials for courses and approaches like this.