12/10/2019 - (last updated: 2019-12-10)

Tutorials link

Part 2: Learning objectives

Select Docker images from Docker Hub

Learn about tags

Use a Docker container to accomplish a task

Review container organization under Linux

Review and use shared directories

Task 1: choosing a Docker image

Docker image example: EMBOSS.

European Molecular Biology Open Software Suite

Search on hub.docker.com

Sort by “Most Popular”:

Task 2: run EMBOSS software

EMBOSS is a software suite of about 250 programs for molecular biology.

We’ll run:

needle a program for pairwise sequence alignment.

pepwheel and pepinfo: protein sequence analysis with graphical output.

We’ll save results in a shared directory (e.g. dockershare.)

Container: 3 access modes

-1. A software inside the container is called to some action.

-2. We now go “inside” the container. New files are lost.

-3. We add a share a folder. All files are saved on local computer.

Methods 1 and 3 are most useful. We’ll test both methods running EMBOSS programs

Getting Started

Reminder

  • Find Terminal in /Applications/Utilities
  • or use Spotlight (top right magnifying glass) and start typing Terminal

bash reminder:

$HOME is a variable representing your home directory, e.g. /Users/yourname

Colored backgrounds

To be more easily distinguish between “where we are looking” the following colored backgrounds are useful:

Green: 
Commands from local computer terminal
Blue: 
Commands and output when WITHIN Docker container
Yellow: 
Informational - DO NOT RUN! - commands or output examples.
White: 
generic output

Docker version & login

docker --version

## Docker version 19.03.5, build 633a0ea

To use Docker beyond that we need to login:

docker login

Supply you Docker username and password.

Review base commands

If you are sitting in front of the same iMac:

List image(s) 
docker images

(Note: same as docker image ls)

List container(s) 
docker container ls
List “stopped” container(s) if any: 
docker container ls -a

If necessary docker stop and delete (docker rm) containers.

Review: pull

Command docker pull assumes tag is latest

latest is Default but not universal!

tag may need to be specified. Example for chosen EMBOSS image:

Note: tag is listed when listing images with docker images

EMBOSS

… Accomplish tasks, see hand-out…

Find EMBOSS on Docker hub.

Run EMBOSS programs in shared folder (i.e. mode 3.)

Run EMBOSS programs from outside container (i.e. mode 1.)

Credits