• docker run with -it and --rm options
• shared directory with -v option
• listing and removing images:
  • docker images
  • docker rmi IMAGE_NAME
• listing and removing containers:
  • docker container ls with optional -a or -aq
  • docker rm CONTAINER_ID to remove a container
• Choosing an image from Docker Hub
• pull images and use appropriate tag if necessary
• We can run a container from within (“dive-in) or without (”remote")

We’ll use 3 images from the Bioinformatics Docker Images Project

• clustalomega - Sequence alignment - (doc)

• fastqc - Sequence read quality assessment - (doc)

• sratoolkit - Operations on Sequence Read Archive SRA database - (doc)

We’ll run clustalomega from outside

We’ll encounter 2 errors:

• FATAL: Cowardly refusing to overwrite already existing file

• unexpected argument "/bin/sh"

This command will fail:

docker run -it --rm pegi3s/clustalomega /bin/sh

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

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

Commands from local computer terminal

Commands and output when WITHIN Docker container

Informational - DO NOT RUN! - commands or output examples.

generic output