PhD Course 2021 - Containers
1
Welcome and about the course
1.1
Meet the organizers and instructors
1.2
About the course
1.2.1
Learning objectives
1.2.2
Prerequisite / technical requirements
1.2.3
Dates, time, location
1.3
Program
2
Introduction to containers
2.1
What are containers ?
2.2
Virtual machines or containers ?
2.2.1
Virtualisation
2.2.2
Containerisation (aka lightweight virtualisation)
2.2.3
Virtual machines vs containers
2.3
History of containers
2.3.1
chroot
2.3.2
Additions in Linux kernel
3
Docker
3.1
Introduction to Docker
3.1.1
What is Docker?
3.1.2
Docker components
3.1.3
Images versus containers
3.1.4
Docker vocabulary
3.2
Using existing images
3.2.1
Getting started
3.2.2
Explore Docker Hub
3.2.3
docker pull: import an image
3.2.4
docker run: run image, i.e. start a container
3.2.5
docker ps: check containers status
3.2.6
docker exec: execute process in a running container
3.2.7
docker stop, start, restart: actions on container
3.2.8
docker rm, docker rmi: clean up!
3.3
Exercise 1 - Docker as a user
3.4
Linux packages
3.4.1
Update and upgrade packages
3.4.2
Search and install packages:
3.5
Docker recipes
3.5.1
Writing recipes and building images
3.5.2
docker tag
3.5.3
Build cache
3.6
Exercise 2 - Docker recipes and build images
3.7
Additional commands
3.8
Volumes
3.9
Ports
3.10
Integrative examples
3.10.1
FASTQC Web Application
3.10.2
Shiny Application
3.11
Publish images
3.11.1
Push an image
3.12
Exercise 3 - Docker volumes and ports
4
Singularity
4.1
Introduction to Singularity
4.1.1
Singularity architecture
4.1.2
Strengths
4.1.3
Weaknesses
4.2
Trivia
4.3
Build process
4.3.1
Examples
4.3.2
Sandboxing
4.3.3
Singularity recipes
4.4
Run and execution process
4.4.1
Singularity shell
4.4.2
Singularity exec
4.4.3
Singularity run
4.4.4
Environment control
4.4.5
Execute from sandboxed images / directories
4.4.6
Execute straight from a registry
4.5
Bind paths (aka volumes)
4.6
Example execution:
4.7
Instances
4.8
Troubleshooting
4.8.1
Fakeroot
4.8.2
Singularity cache directory
4.8.3
Global singularity configuration
4.9
Exercise 4 - Singularity running and building
4.9.1
Blast command-line (1)
4.9.2
Blast command-line (2)
BIOINFORMATICS CORE @ CRG
PhD Course 2021: Linux containers in scientific environments
1.1
Meet the organizers and instructors
Contacts below:
CRG Training unit:
Damjana
Anna
Main speakers:
Toni
Instructors/helper:
Luca
Julia