3 Containers

Linux containers

What are containers?

A Container can be seen as a minimal virtual environment that can be used in any Linux-compatible machine (and beyond).

Using containers is time- and resource-saving as they allow:

• Controlling for software installation and dependencies.

• Reproducibility of the analysis.

Containers allow us to use exactly the same versions of the tools.

Virtual machines or containers ?

Virtualisation	Containerisation (aka lightweight virtualisation)
Abstraction of physical hardware	Abstraction of application layer
Depends on hypervisor (software)	Depends on host kernel (OS)
Do not confuse with hardware emulator	Application and dependencies bundled all together
Enable virtual machines	Every virtual machine with an OS (Operating System)

Virtual machines vs containers

Source

Pros and cons

ADV	Virtualisation	Containerisation
PROS.	Very similar to a full OS. High OS diversity	No need of full OS installation (less space). Better portability Faster than virtual machines. Easier automation. Easier distribution of recipes. Better portability.
CONS.	Need more space and resources. Slower than containers. Not that good automation.	Some cases might not be exactly the same as a full OS. Still less OS diversity, even with current solutions

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:22.04

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:22.04 /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:22.04 /bin/whoami
docker run ubuntu:22.04 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.

With --name you can provide a name to the container.

docker run -it ubuntu:22.04 /bin/bash

docker run --name myubuntu -it ubuntu:22.04 /bin/bash

docker ps: check containers status

List running containers:

docker ps

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

docker ps -a

docker rm, docker rmi: clean up!

docker rm myubuntu
docker rm -f myubuntu

docker rmi ubuntu:22.04

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 data
# We can also copy the FASTQ we used in data
docker run --volume $(pwd)/data:/scratch --name fastqc_container biocontainers/fastqc:v0.11.9_cv7 fastqc /scratch/B7_input_s_chr19.fastq.gz

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

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 data
# We can copy some FASTQ in data
docker run --volume $(pwd)/data:/scratch --name fastqc_container biocontainers/fastqc:v0.11.9_cv7 fastqc /scratch/B7_input_s_chr19.fastq.gz

Singularity

• Focus:

  • Reproducibility to scientific computing and the high-performance computing (HPC) world.

• Origin: Lawrence Berkeley National Laboratory. Later spin-off: Sylabs

• Version 1.0 -> 2016

• More information: https://en.wikipedia.org/wiki/Singularity_(software)

Singularity architecture

Strengths	Weaknesses
No dependency of a daemon	At the time of writing only good support in Linux
Can be run as a simple user	Mac experimental. Desktop edition. Only running
Avoids permission headaches and hacks	For some features you need root account (or sudo)
Image/container is a file (or directory)
More easily portable
Two types of images: Read-only (production)
Writable (development, via sandbox)

Trivia

Nowadays, there may be some confusion since there are two projects:

• Apptainer Singularity

• Sylabs Singularity

They “forked” in 2021. So far they share most of the codebase, but eventually this could be different, and software might have different functionality.

The former is already “End Of Life” and its development continues named as Apptainer, under the support of the Linux Foundation.

Container registries

Container images, normally different versions of them, are stored in container repositories.

These repositories can be browser or discovered within, normally public, container registries.

Docker hub

It is the first and most popular public container registry (which provides also private repositories).

• Docker Hub

Example:

https://hub.docker.com/r/biocontainers/fastqc

singularity build fastqc-0.11.9_cv7.sif docker://biocontainers/fastqc:v0.11.9_cv7

Biocontainers

• Biocontainers

Website gathering Bioinformatics focused container images from different registries.

Originally Docker Hub was used, but now other registries are preferred.

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

Via quay.io

https://quay.io/repository/biocontainers/fastqc

singularity build fastqc-0.11.9.sif docker://quay.io/biocontainers/fastqc:0.11.9--0

Via Galaxy project prebuilt images

singularity pull --name fastqc-0.11.9.sif https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0

Galaxy project provides all Bioinformatics software from the BioContainers initiative as Singularity prebuilt images. If download and conversion time of images is an issue, this might be the best option for those working in the biomedical field.

Link: https://depot.galaxyproject.org/singularity/

Running and executing containers

Once we have some image files (or directories) ready, we can run processes.

Singularity shell

The straight-forward exploratory approach is equivalent to docker run -ti biocontainers/fastqc:v0.11.9_cv7 /bin/sh but with a more handy syntax.

singularity shell fastqc-0.11.9.sif

Move around the directories and notice how the isolation approach is different in comparison to Docker. You can access most of the host filesystem.

Singularity exec

That is the most common way to execute Singularity (equivalent to docker exec). That would be the normal approach in a HPC environment.

singularity exec fastqc-0.11.9.sif fastqc

a processing of a FASTQ file from data directory:

singularity exec fastqc-0.11.9_cv7.sif fastqc B7_input_s_chr19.fastq.gz

Environment control

By default Singularity inherits a profile environment (e.g., PATH environment variable). This may be convenient in some circumstances, but it can also lead to unexpected problems when your own environment clashes with the default one from the image.

singularity shell -e fastqc-0.11.9.sif
singularity exec -e fastqc-0.11.9.sif fastqc

Compare env command with and without -e modifier.

singularity exec fastqc-0.11.9.sif env
singularity exec -e fastqc-0.11.9.sif env

Exercise

Using the 2 fastq available files, process them using fastqc.

Suggested solution

# Let's create a dummy directory
mkdir data

# Let's copy contents FASTQC files in data directory

singularity exec fastqc.sif fastqc data/*fastq.gz

# Check you have some HTMLs there. Remove them
rm data/*html

# Let's use shell
singularity shell fastqc.sif
> cd data
> fastqc *fastq.gz
> exit