Docker

Introduction to Docker

What is Docker?

• Platform for developing, shipping and running applications.

• Infrastructure as application / code.

• First version: 2013.

• Company: originally dotCloud (2010), later named Docker.

• Established Open Container Initiative.

As a software:

• Docker Community Edition.

• Docker Enterprise Edition.

There is an increasing number of alternative container technologies and providers. Many of them are actually based on software components originally from the Docker stack and they normally try to address some specific use cases or weakpoints. As a example, Singularity, that we introduce later in this couse, is focused in HPC environments. Another case, Podman, keeps a high functional compatibility with Docker but with a different focus on technology (not keeping a daemon) and permissions.

Docker components

• Read-only templates.

• Containers are run from them.

• Images are not run.

• Images have several layers.

Images versus containers

• Image: A set of layers, read-only templates, inert.

• An instance of an image is called a container.

When you start an image, you have a running container of this image. You can have many running containers of the same image.

“The image is the recipe, the container is the cake; you can make as many cakes as you like with a given recipe.”

https://stackoverflow.com/questions/23735149/what-is-the-difference-between-a-docker-image-and-a-container

Docker vocabulary

docker

Get help:

docker run --help

Using existing images

Explore Docker hub

Images can be stored locally or shared in a registry.

Docker hub is the main public registry for Docker images.

Let’s search the keyword ubuntu:

docker pull: import image

• get latest image / latest release

docker pull ubuntu

• choose the version of Ubuntu you are fetching: check the different tags

docker pull ubuntu:18.04

Biocontainers

https://biocontainers.pro/

Specific directory of Bioinformatics related entries

• Entries in Docker hub and/or Quay.io (RedHat registry)

• Normally created from Bioconda

Example: FastQC

https://biocontainers.pro/#/tools/fastqc

docker pull biocontainers/fastqc:v0.11.9_cv7

docker images: list images

docker images

Each image has a unique IMAGE ID.

docker run: run image, i.e. start a container

Now we want to use what is inside the image.

docker run creates a fresh container (active instance of the image) from a Docker (static) image, and runs it.

The format is:

docker run image:tag command

docker run ubuntu:18.04 /bin/ls

Now execute ls in your current working directory: is the result the same?

You can execute any program/command that is stored inside the image:

docker run ubuntu:18.04 /bin/whoami
docker run ubuntu:18.04 cat /etc/issue

You can either execute programs in the image from the command line (see above) or execute a container interactively, i.e. “enter” the container.

docker run -it ubuntu:18.04 /bin/bash

Run container as daemon (in background)

docker run --detach ubuntu:18.04 tail -f /dev/null

Run container as daemon (in background) with a given name

docker run --detach --name myubuntu ubuntu:18.04 tail -f /dev/null

docker ps: check containers status

List running containers:

docker ps

List all containers (whether they are running or not):

docker ps -a

Each container has a unique ID.

docker exec: execute process in running container

docker exec myubuntu uname -a

• Interactively

docker exec -it myubuntu /bin/bash

docker stop, start, restart: actions on container

Stop a running container:

docker stop myubuntu

docker ps -a

Start a stopped container (does NOT create a new one):

docker start myubuntu

docker ps -a

Restart a running container:

docker restart myubuntu

docker ps -a

Run with restart enabled

docker run --restart=unless-stopped --detach --name myubuntu2 ubuntu:18.04 tail -f /dev/null

• Restart policies: no (default), always, on-failure, unless-stopped

Update restart policy

docker update --restart unless-stopped myubuntu

docker rm, docker rmi: clean up!

docker rm myubuntu
docker rm -f myubuntu

docker rmi ubuntu:18.04

Major clean

Check used space

docker system df

Remove unused containers (and others) - DO WITH CARE

docker system prune

Remove ALL non-running containers, images, etc. - DO WITH MUCH MORE CARE!!!

docker system prune -a

• Reference: https://www.digitalocean.com/community/tutorials/how-to-remove-docker-images-containers-and-volumes

Exercise

• • Imagemagick

• Pull the imagemagick image from: https://hub.docker.com/r/acleancoder/imagemagick-full

• Check the version of the convert command.

• Start a container interactively.

• Inside the container: download this png image (https://www.docker.com/wp-content/uploads/2022/03/vertical-logo-monochromatic.png)

• Convert it to .jpg using the convert command of imagemagick (format; convert image.png image.jpg).

• Exit the container.

• Copy the jpg image back from the stopped container! Try new command docker cp.

Suggested solution

# Pull image
docker pull acleancoder/imagemagick-full

# Check version of `convert`
docker run acleancoder/imagemagick-full convert --version

# Start interactive container
docker run -it acleancoder/imagemagick-full
  # fetch png image
  > wget  https://www.docker.com/wp-content/uploads/2022/03/vertical-logo-monochromatic.png
  # convert to jpg
  > convert vertical-logo-monochromatic.png myimage.jpg
  # exit container

# fetch container ID with `ps -a` and use `docker cp` to copy jpg file from the stopped container to the host
docker cp *CONTAINER_ID*:/myimage.jpg .

Volumes

Docker containers are fully isolated. It is necessary to mount volumes in order to handle input/output files.

Syntax: –volume/-v host:container

mkdir datatest
touch datatest/test
docker run --detach --volume $(pwd)/datatest:/scratch --name fastqc_container biocontainers/fastqc:v0.11.9_cv7 tail -f /dev/null
docker exec -ti fastqc_container /bin/bash
> ls -l /scratch
> exit

Ports

The same as with volumes, but with ports, to access Internet services.

Syntax: –publish/-p host:container

docker run --detach --name webserver nginx
curl localhost:80
docker exec webserver curl localhost:80
docker rm -f webserver

docker run --detach --name webserver --publish 80:80 nginx
curl localhost:80
docker rm -f webserver

docker run --detach --name webserver -p 8080:80 nginx
curl localhost:80
curl localhost:8080
docker exec webserver curl localhost:80
docker exec webserver curl localhost:8080
docker rm -f webserver

Volume exercises

1. Copy the 2 fastq files from available datasets in Github repository and place them in mounted directory

2. Run fastqc interactively (inside container): `fastqc  /scratch/*.gz`

3. Run fastqc non-interactively (outside the container)

docker run –user

It is possible to run certain containers with a specific user, appending `run --user`.

A convenient command would be:

docker run --user $(id -u):$(id -g) --detach --volume $(pwd)/datatest:/scratch --name user_test biocontainers/fastqc:v0.11.9_cv7 touch /scratch/userfile