12/10/2019 - (last updated: 2019-12-10)
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
Docker image example: EMBOSS.
European Molecular Biology Open Software Suite
Search on hub.docker.com
Sort by “Most Popular”:
EMBOSS is a software suite of about 250 programs for molecular biology.
needle a program for pairwise sequence alignment.
pepinfo: protein sequence analysis with graphical output.
We’ll save results in a shared directory (e.g.
-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.
$HOME is a variable representing your home directory, e.g.
To be more easily distinguish between “where we are looking” the following colored backgrounds are useful:Green:
Commands from local computer terminal
Commands and output when WITHIN Docker container
Informational - DO NOT RUN! - commands or output examples.
## Docker version 19.03.5, build 633a0ea
To use Docker beyond that we need to login:
Supply you Docker username and password.
If you are sitting in front of the same iMac:List image(s)
(Note: same as
docker image ls)
docker container ls
docker container ls -a
docker stop and delete (
docker rm) containers.
docker pull assumes tag is
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
… 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.)
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Docker logo from www.kissclipart.com
Illustration images from pixabay.com, pexels.com/