Docker: GETTING STARTED

A hands-on step-by-step basic guide to Docker essentials.

Developed by

The H3ABionet Pipelines and Computing Work Package,

Computing Infrastructure project team

Prepared for the greater

H3ABioNet and H3Africa Consortium communities

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Document Control
Date Version Notes
1.0 Initial guide development

Project Members
Last Name First Name Institution Country
Ghanmi Nidhal Institute of Pasteur , Tunis Tunisia
Lukyamuzi Edward Uganda Virus Research Institute Uganda
Maslamoney Suresh Computational Biology Division, University South Africa
of Cape Town
Meintjes Ayton Computational Biology Division, University South Africa
of Cape Town
Oloyede Emmnauel National Biotechnology Development Nigeria
Agency
Wamala Timothy Uganda Virus Research Institute Uganda

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Project Members .................................................................................................................................. 2
Abbreviations ........................................................................................................................................ 5
1. What are Containers? ...................................................................................................................... 5
1.1 Types of Containers ...................................................................................................................... 7
1.1.1 Popular Container Providers 7
1.2 What is Docker .............................................................................................................................. 7
1.3 When to Use Docker ..................................................................................................................... 7
1.4 When Not to Use Docker .............................................................................................................. 8
1.5 Core Components of Docker ......................................................................................................... 8
1.6 Docker Terminology ...................................................................................................................... 9
1.7 Docker Editions ........................................................................................................................... 10
2. Installing Docker CE on Ubuntu 20.04/20.04 LTS ............................................................................. 10
2.1. Install Using Advanced Packaging Tool (APT) ............................................................................ 10
2.2 Install Using Snap ........................................................................................................................ 11
3. Getting Started.................................................................................................................................. 12
3.1 Basic Commands ......................................................................................................................... 12
4. Docker Images................................................................................................................................... 14
5. Docker Registry ................................................................................................................................. 15
6. Docker Networking ........................................................................................................................... 16
6.1 Bind Host Port to container Port................................................................................................. 16
7. Docker Volumes ................................................................................................................................ 16
7.1 Get Started with Volumes ........................................................................................................... 16
8. Docker Applications .......................................................................................................................... 17
8.1 Static site on nginx server from Docker ...................................................................................... 17

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Background
This guide is produced by the Computing & Infrastructure working group under the Pipelines and
Computing work package. It is intended to serve as a self-sufficient support guide on all major
aspects around docker technology for system administrators across the H3ABioNet and its
collaborating partners. All commands and screenshots are based on the Ubuntu 20.04 Operating
System (OS). The guide has been designed to be effective as a standalone self-guided walkthrough
of installing, deploying and management of docker containers- while the guide is written in an easy
to read, user-friendly way, it assumes familiarity with navigating around an Ubuntu 20.04 Linux
system. If you are not familiar with Linux, refer to our “LINUX: GETTING STARTED” guide on the
https://h3abionet.org/tools-and-services/technical-guidelines website. Following the instructions in
this guide will give the reader hands on experience with installing the Docker community edition,
create a basic Docker container with a static web page. It includes useful commands to manage
multiple containers and images.

It is recommended that the reader first reads this guide in its entirety before following the
step by step instructions.

This guide makes the following assumptions:

• The reader is comfortable navigating the Ubuntu 20.04 Linux OS

• Is able to install software and edit files at the command line

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How to read this guide
• General text describing each section and commands are written in the Arial font, size
11. This text is to be read to understand which skills will be gained in the following
section and to describe the command operation.
• When noting a variation to a default command or to note a point or warning, the
default text will be highlighted in yellow.
• When noting a tip, for example, a command that can be run in multiple ways
producing the same output, this text will be highlighted in green.
• When giving examples of actual expected output, this text will be highlighted with a
grey background.
• When listing a command that is to be run by the reader to produce an output, the
command will be in light blue italics.

Abbreviations
Abbreviation Description
OS Operating System
cli Command line interface
gui Graphical user interface
dhcp Dynamic host configuration protocol
IP Internet Protocol
VM Virtual Machine

1. What are Containers?

In the recent past, the industry standard was to use Virtual Machines (VMs) to run software
applications. VMs run applications inside a guest Operating System, which runs on virtual hardware
powered by the host server’s OS.

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VMs are great at providing full process isolation for applications: there are very few ways a problem
in the host operating system can affect the software running in the guest operating system, and vice-
versa. But this isolation comes at great cost — the computational overhead spent virtualizing
hardware for a guest OS to use is substantial.

Containers take a different approach, by leveraging the low-level mechanics of the host operating
system, containers provide most of the isolation of virtual machines at a fraction of the computing
power.

Essentially, Docker is a container-based system for your applications. If you’re used to the concept of
virtual servers, Docker provides further levels of abstraction for your application. Here’s a visual
representation of how containers differ from VMs:

Image Source: https://blog.netapp.com/

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1.1 Types of Containers
Linux Containers (LXC) — The original Linux container technology is Linux Containers, commonly
known as LXC. LXC is a Linux operating system level virtualization method for running multiple isolated
Linux systems on a single host.

Docker — Docker started as a project to build single-application LXC containers, introducing several
changes to LXC that make containers more portable and flexible to use. It later morphed into its own
container runtime environment. At a high level, Docker is a Linux utility that can efficiently create,
ship, and run containers.

1.1.1 Popular Container Providers

1. Linux Containers
● LXC
● LXD
● CGManager
2. Docker
3. Singularity
4. Windows Server Containers

1.2 What is Docker

Unless you’ve been living without internet access for the last years, it would be hard not to at least
have heard of Docker. But as an emerging technology, not everyone has taken the time to work out
what Docker is, where it fits in, and how it can benefit you.

So, what exactly is Docker? Here’s how Docker themselves describe it:

“Docker is an open platform for developers and sysadmins of distributed applications.”

Wikipedia defines Docker as:

“an open-source project that automates the deployment of software applications

inside containers by providing an additional layer of abstraction and automation of OS-level
virtualization on Linux.”
Wow! That's a mouthful. In simpler words, Docker is a tool that allows developers, sysadmins etc. to
easily deploy their applications in a sandbox (called containers) to run on the host operating system
i.e. Linux. The key benefit of Docker is that it allows users to package an application with all of its
dependencies into a standardized unit for software development. Unlike virtual machines, containers
do not have high overhead and hence enable more efficient usage of the underlying system and
resources.

1.3 When to Use Docker

If your application fits into one or more of the following categories, Docker may be a good fit:

Learning new technologies: To get started with a new tool without spending time on installation and
configuration, Docker offers an isolated and disposable environment. Many projects maintain Docker
images with their applications already installed and configured.

Basic use cases: Pulling images from Docker Hub is also a good solution if your application is basic or
standard enough to work with a default Docker image. Cases such as hosting a website using a LAMP

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stack or using a reverse proxy have an official or well-supported image available on DockerHub. If the
default configuration in these images is acceptable for your needs, then pulling the image can save a
lot of time that would otherwise be spent setting up your environment and installing the necessary
tools.

App isolation: If you want to run multiple applications on one server, keeping the components of each
application in separate containers will prevent problems with dependency management.

Developer teams: If you have developers working with different setups, Docker provides a convenient
way to have local development environments that closely match the production environment, without
needing to ssh into a remote box.

1.4 When Not to Use Docker

There are also times when Docker isn’t the best solution. Here are some examples:

Your app is complicated and you are not/do not have a sysadmin. For large or complicated
applications, using a pre-made Dockerfile or pulling an existing image will not be sufficient. Building,
editing, and managing communication between multiple containers on multiple servers is a time-
consuming task.

Performance is critical to your application. Docker shines compared to virtual machines when it
comes to performance because containers share the host kernel and do not emulate a full operating
system. However, Docker does impose performance costs. Processes running within a container will
not be quite as fast as those run on the native OS. If you need to get the best possible performance
out of your server, you may want to avoid Docker.

Security is critical to your application. As mentioned above, keeping the different components of an
application in separate containers provides some security benefits, since a compromise in one
container can’t easily affect the rest of your system. However, Docker’s containerization approach
raises its own security challenges, especially for more complicated applications. These issues are
solvable but require attention from an experienced security engineer.

Multiple operating systems. Since Docker containers share the host computer’s operating system, if
you want to run or test the same application on different operating systems, you will need to use
virtual machines instead of Docker.

Clusters. Docker containers on separate servers can be combined to form a cluster with Docker
Swarm. However, Docker does not take the place of provisioning or automation tools such as Ansible,
SaltStack, and Chef. In addition, Docker support Kubernetes, hinting that Docker Swarm may not be
sufficient as a stand-alone cluster manager.

1.5 Core Components of Docker

Docker Engine is one of the core components of Docker. It is responsible for the overall functioning of
the Docker platform.

Docker Engine is a client-server based application and consists of 3 main components.

● Server
● REST API
● Client

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 Image Source: https://docs.docker.com

The Server runs a daemon known as dockerd (Docker Daemon), which is nothing but a process. It is
responsible for creating and managing Docker Images, Containers, Networks and Volumes on the
Docker platform.

The REST API specifies how the applications can interact with the Server, and instruct it to get their
job done.

The Client is nothing but a command line interface, that allows users to interact with Docker using the
commands.

1.6 Docker Terminology

Let us take a quick look at some of the terminology associated with Docker.

Docker Images and Docker Containers are the two essential things that you will come across daily
while working with Docker.

In simple terms, a Docker Image is a template that contains the application, and all the dependencies
required to run that application on Docker.

On the other hand, as stated earlier, a Docker Container is a logical entity. In more precise terms, it is
a running instance of the Docker Image.

What is Docker Hub?

Docker Hub is the official online repository where you could find all the Docker Images that are
available for us to use.

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Docker Hub also allows us to store and distribute our custom images as well if we wish to do so. We
could also make them either public or private, based on our requirements.

1.7 Docker Editions

Docker is available in 2 different editions, as listed below:

● Community Edition (CE)

● Enterprise Edition (EE)

The Community Edition is suitable for individual developers and small teams. It offers limited
functionality, in comparison to the Enterprise Edition.

The Enterprise Edition, on the other hand, is suitable for large teams and for using Docker in
production environments.

The Enterprise Edition is further categorized into three different editions, as listed below:

● Basic Edition
● Standard Edition
● Advanced Edition

2. Installing Docker CE on Ubuntu

20.04/20.04 LTS
Let's explore the use of the Advanced Packaging Tool (APT) and Snap to install docker on Ubuntu 20.04
LTS. In recent years a new package management system called Snap has been under development by
the Ubuntu team at Canonical, Ltd. Although there are no official plans to replace APT entirely with
Snap, the list of packages that can now be installed as “snaps” continues to grow

2.1. Install Using Advanced Packaging Tool (APT)

First, update your existing list of packages: the system needs to be updated to make it safer and
reliable to install Docker.

$ sudo apt update

Install Prerequisite Packages

Once we have updated the system, we need to install some necessary packages before we are ready
to install Docker.

$ sudo apt install curl apt-transport-https ca-certificates software-properties-common

Add the Docker Repositories

This enables us to use the officially supported method of the installation making the installation
process much easier.

First add the GPG key for the official Docker repository to your system:

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 $ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add –

Then, Add the Docker repository to APT sources:

$sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu

$(lsb_release -cs) stable"

Next, update the package database with the Docker packages from the newly added repo:

$ sudo apt update

Make sure you are installing from the Docker repo instead of the default Ubuntu repo with this
command:

$ apt-cache policy docker-ce

Install Docker: Use the apt command

$sudo apt install docker-ce

$ sudo service docker start

Check the docker status: good idea to check that it’s running

$ sudo systemctl status docker

Add Docker service to the system startup: so that it will start automatically on system boot.

$ sudo systemctl enable docker

Check the docker version

$ docker --version

Optional : Add current user to docker group to avoid using sudo

$ sudo usermod -aG docker ubuntu

Give Permissions to current user to execute docker binary

$ sudo chmod 755 /usr/bin/docker

2.2 Install Using Snap

Snap packages are universal Linux packages that make it easy to deploy applications/software on any
Linux distribution.

Let's see how to manage Docker installation using Snap

First step is to check versions available for Docker in Snap packages

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 $ snap info docker

Next is to install docker using one of the channels (deployment packages) available

$ sudo snap install docker

Verify that docker has been installed

$ snap services docker

It prints service name as 'docker.dockerd' that is different from service name when you deploy
without using Snap package

Start docker
$ sudo snap start docker
Stop docker installed using Snap package
$ sudo snap stop docker
To uninstall or remove docker installed using Snap package
$ sudo snap remove docker

3. Getting Started
3.1 Basic Commands
Info command: gives information about the docker setup on your machine/vm

$ docker info

Run Container and enter its shell

$ sudo docker run -i -t ubuntu /bin/bash

This should give you a new command prompt inside the container, very similar to if you had ssh‘ed
into a remote machine. In this case the flags -i and -t tell Docker we want an interactive session with
a tty attached. The command /bin/bash gives a bash shell. When you exit the shell the container will
stop — containers only run as long as their main process
$ docker run ubuntu echo hello-world
hello-world

Run Container and enter its shell: use -h command line parameter to specify a container name.

$ docker run -h CONTAINER1 -i -t ubuntu /bin/bash

Output of the command above will open a tty inside the container
root@CONTAINER1:/#

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Run Container with Networking mode: use the flag --net

$ docker run -h CONTAINER2 -i -t --net="bridge" ubuntu /bin/bash

List of docker containers running

$ docker ps -a

Inspect a Container

$ docker inspect CONTAINER_NAME

Start a Stopped Container

$ docker start CONTAINER_NAME

Enter the Shell of a Started Container

$ docker attach CONTAINER_NAME
where CONTAINER_NAME is the container name.
Delete a Container

docker rm CONTAINER_NAME
Detach from a Container

docker run -t -i → can be detached with ^P^Q and reattached with docker attach
docker run -i → cannot be detached with ^P^Q; will disrupt stdin
docker run → cannot be detached with ^P^Q;
can SIGKILL client; can reattach with docker attach

Docker Logs: get a list of commands executed in the container.

$ docker logs CONTAINER_NAME

Pause a Container: Note : Container needs to be in the Started Phase

$ docker pause CONTAINER_NAME

UnPause a Paused Container

$ docker unpause CONTAINER_NAME

Removing all the Containers

$ docker rm `docker ps --no-trunc -aq`

List Docker Networks

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 $ docker network ls

Rename a Docker Container

$ docker rename OLD_NAME NEW_NAME

4. Docker Images
Show images
$ sudo docker images

Specifying a Variant
$ sudo docker run -i -t ubuntu:20.04 /bin/bash

Pull an Image
$ sudo docker pull ubuntu

Create your own image

Make a docker file directory

$ mkdir docker-file

Make a docker file

$ cd docker-file/
$ touch Dockerfile

Add content to docker file

$ cat > Dockerfile

FROM ubuntu:20.04
MAINTAINER xyz "xyz@xyz.com"
RUN apt-get update
RUN apt-get install -y nginx
RUN echo 'Our first Docker image for Nginx' > /usr/share/nginx/html/index.html
EXPOSE 80

Ctrl+D to save the changes

Creating a image

Build a docker image

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 $ sudo docker build -t="test/my_nginx"

Check that image has been created

$ docker images | grep nginx

test/my_nginx
Removing a Docker Image
$ docker rmi test/my_nginx

5. Docker Registry
Docker allows to bundle and push the customized images on the docker hub or locally hosted docker
registry. Images can be pushed or pulled from this registry.
Create official Docker Hub account
$ sudo docker login
Username: username
Password:
Email: email@example.com
WARNING:login credentials saved in /home/username/.dockercfg.
Account created. Please use the confirmation link we sent to your e-mail to activate it.

Search publicly available images in the Docker hub registry: e.g with keyword “centos”
$ sudo docker search centos

Push customized image to Docker repository: make sure repository name meets the username of the
docker hub account in order to push the images
$ sudo docker push username/newimage

Install Private Local Docker Registry

$ docker run -p 5000:5000 registry

Tag the images

Now, we will the tag the same image created in the above tutorial to “localhost:5000/newimage” so
that the repository name matches and it can be easily pushed to private docker registry.
$docker tag username/newimage:latest localhost:5000/newimage:latest

Push the image to private docker registry

$ docker push localhost:5000/newimage:latest

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6. Docker Networking
6.1 Bind Host Port to container Port
Run the previously created my_ngnix with port binding

$ sudo docker run -d -p 8080:80 --name test_container test/my_nginx nginx -g "daemon

off;"

The -p 8080:80 option will bind the host port 8080 to the container port 80. So we will be
able to see the default web page of “Our first Docker image for Nginx” by simply visiting the
IP address of our docker host.

$ curl http://docker-host-ip:8080

7. Docker Volumes
7.1 Get Started with Volumes
Let us see how to create a basic docker volume and mount it in a container

Volume mounted in a container

1. Use -v parameter
$ docker run -v /volume1 -i -t ubuntu /bin/bash

2. Verify existence of volume using ls command

$root@b979b5d735b0:/# ls
bin boot dev etc home lib lib64.. var volume1

Mount a Host Directory as a Volume

1. Create a local directory /host/logs
$ sudo mkdir -p /host/logs
$ sudo touch /host/logs/log1.txt
2. Bind /host/logs host directory to /container/logs volume
$ docker run -v /host/logs:/container/logs -i -t ubuntu /bin/bash
3. Execute ls to see the contents of mounted volume. The contents are the same as created in
host directory.
root@3774005dee32:/# ls
bin boot container .. srv sys tmp usr var
root@3774005dee32:/# ls container/logs/

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 log1.txt

8. Docker Applications
8.1 Static site on nginx server from Docker
Let’s host a static site running on nginx server hosted by Docker
1. Create a Dockerfile
FROM ubuntu:20.04
RUN apt-get update
RUN apt-get install nginx -y
COPY index.html /var/www/html/
EXPOSE 80
CMD [“nginx”, “-g”, “daemon off:”]

2. Create a directory public_html with the following content in index.html

<html>
<h1>Hello World!</h1>
<p>Hi there – This is a simple static website!</p>
</html>
3. Your directory should look like this
$ tree .
.
├── Dockerfile
└── public_html
└── index.html
4. Create a Docker image
$ docker build -t my-nginx .

5. Create a Docker Container running this image

$ docker run -p 80:80 --name my-nginx-01 my-nginx

6. Open browser of the host at http://localhost:80, you will see the website up and running

Should you have any comments or recommendations regarding this guide, please drop us a note on
our helpdesk at helpdesk@h3abionet.org.

--oOo END oOo--

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