Installing DLATK with Docker

Run from Docker Hub

Step 1: Install Docker

Installing Docker is very easy. Visit the official Docker installation page page and follow the instructions tailored for your operating system.

After you’ve installed Docker, open the terminal and type the following to verify the installation:

> docker info

you should see something like

> docker info
Containers: 0
 Running: 0
 Paused: 0
 Stopped: 0
Images: 0
...

Step 2: Install MySQL

You can pull the offical image of MySQL from Docker Hub. Starting a MySQL instance is simple:

> docker run --name some-mysql --env MYSQL_ROOT_PASSWORD=my-secret-pw --detach mysql:tag

where some-mysql is the name you want to assign to your container, my-secret-pw is the password to be set for the MySQL root user and tag is the tag specifying the MySQL version you want. We've tested using MySQL v5.5:

> docker run --name mysql_v5  --env MYSQL_ROOT_PASSWORD=my-secret-pw --detach mysql:5.5

and we can confirm the installation with:

> docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
mysql               5.5                 a8a59477268d        7 weeks ago         445MB

> docker ps
CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS                    NAMES
552954e73844        mysql               "docker-entrypoint..."   5 minutes ago       Up 5 minutes        0.0.0.0:3306->3306/tcp   mysql_v5

Note that this is running on port 3306. Here is the command broken down:

  • run: Run a command in a new container.
  • --name: Assign a name to the container. If you don’t specify this, Docker will generate a random name.
  • --env: Set environment variables
  • --detach: Run container in background and print container ID
  • mysql: The image name as stated on the Docker Hub page. This is the simplest image name. The standard is “username/image_name:tag”, for example “severalnines/mysql:5.6”. In this case, we specified “mysql”, which means it has no username (the image is built and maintained by Docker, therefore no username), the image name is “mysql” and the tag is latest (default). If the image does not exist, it will pull it first from Docker Hub into the host, and then run the container.

You can see which IP the MySQL container is running on via:

> docker inspect mysql_v5 | grep IPAddress
    "SecondaryIPAddresses": null,
    "IPAddress": "172.17.0.2",
            "IPAddress": "172.17.0.2",

Both of these can be used to configure a graphical SQL client such as Heidi, MySQL Workbench or Sequel Pro.

To open this MySQL instance we run, remembering that we set the root password to my-secret-pw:

> docker exec -it mysql_v5 bash

root@d6ed6aa86c31:/# mysql -p
Enter password:

Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 13
Server version: 8.0.11 MySQL Community Server - GPL

Copyright (c) 2000, 2018, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
4 rows in set (0.00 sec)

mysql>

Build Image from DockerFile

This is more advanced and probably not needed for most use cases. First we download the DockerFile from GitHub. If you have git installed you can run

> git clone https://github.com/dlatk/dlatk-docker.git && cd dlatk-docker

To build the image we run:

> docker build -t dlatk-docker .

Here is the command broken down:

  • build: Build an image from a Dockerfile
  • -t: Alias for --tag. Name and optionally a tag in the 'name:tag' format. Since we are not specifying a tag we will pull the latest version.

You will see the following output:

Sending build context to Docker daemon  84.48kB
Step 1/15 : FROM python:3.6-stretch
stretch: Pulling from library/python
cc1a78bfd46b: Downloading [=============================================>     ]  40.86MB/45.32MB
d2c05365ee2a: Download complete
231cb0e216d3: Download complete
3d2aa70286b8: Downloading [===================================>               ]  35.08MB/50.06MB
e80dfb6a4adf: Downloading [=======>                                           ]  31.16MB/213.2MB
....

At the end you should see:

Removing intermediate container c4776548e966
Successfully built dc2005cd24a6
Successfully tagged dlatk-docker:latest

and we can confirm the installation with:

> docker images
docker images
REPOSITORY          TAG                 IMAGE ID            CREATED              SIZE
dlatk-docker        latest              10eea3e0202a        About a minute ago   2.56GB
python              3.6-stretch         d330010a503a        3 days ago           912MB

Acknowledgment

The DockerFile was originally written by Michael Becker at Penn Medicine.