Introduction to Docker and Singularity

Introduction to Docker
8 Topics
Background about Docker
Docker components
Docker vocabulary
Container Setup explained
Basics of the Docker images
What is Containerization?
Advantages of Docker
Typical use cases
Using existing images
13 Topics
Explore Docker hub
Exercise on getting images
Get tools from Biocontainers
List docker images
Starting an image with docker run
Run container as daemon
Check containers status via docker ps
Clean up the containers and the images
Execute a process in running container
Summary
Volumes
Excercise with volumes
Ports
Docker recipes: build your own images
12 Topics
Building the recipes for images
More advanced image building
Building cache
Tagging the images
Starting the build
More instructions for the recipes
One tool, one image or some tools, one image
General recommendations
Dockerfile tips
Getting an image to Docker Hub
Inspecting Dockerfiles created by other parties
Using Biocontainers and Bioconda for bioinformatics tools
Introduction to Singularity
6 Topics
Background about Singularity
Strengths and Weaknesses
Singularity Architecture
Getting started
Singularity’s Image Cache
Using existing Singularity images
Run and execute Singularity images
6 Topics
Using the Singularity containers to run commands
Files in Singularity containers
Binding local folders (aka volumes)
Using Docker images with Singularity
Run from sandbox container or remotely
Troubleshooting options
Building Singularity images
4 Topics
Building Singularity images
Change the image via sandbox
Using singularity recipes
Remotely building
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Building cache

Introduction to Docker and Singularity Docker recipes: build your own images Building cache

Every line of a Dockerfile is actually an image/layer by itself.

Modify for instance the last bit of the previous image (let’s change the image URL) and rebuild it (even with a different name/tag):

FROM ubuntu:18.04

MAINTAINER Toni Hermoso Pulido <toni.hermoso@crg.eu>

WORKDIR ~

RUN apt-get update && apt-get -y upgrade
RUN apt-get install -y wget

ENTRYPOINT ["/usr/bin/wget"]
CMD ["https://cdn-images-1.medium.com/max/1600/1*_NQN6_YnxS29m8vFzWYlEg.png"]
docker build -t mytestimage2 .

It will start from the last line. This is OK most of the times and very convenient for testing and trying new steps, but it may lead to errors when versions are updated (either FROM image or included packages). For that it is benefitial to start from scratch with --no-cache tag.

docker build --no-cache -t mytestimage2 .
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