Set-up

The user needs to belong to the group docker. The following command lets you check this:

Terminal

groups username

If the output is something like username : username docker you are good to go. It means that the user is part of the groups username and docker. (A group with the same name as the user is always created while creating the user.)

If you do not belong to the group docker, consult your system admin. Basically, this is the person with the sudo privilages on your server. You will be added to the docker group with the command below (ref):

Terminal

sudo usermod -aG docker username

-a means to append the group (docker above) to the list of groups a user is associated with -G means a comma separated list of groups (none above)

Pulling a docker image

You will need to “pull” a docker image (basically a template) and then start a docker container based on the pulled image.

Terminal

docker image pull ...

You can inspect pulled/downloaded images with the following code:

Terminal

docker image ls

The output of docker image ls would be something like the following:

REPOSITORY                                    TAG       IMAGE ID       CREATED        SIZE
quay.io/comparative-genomics-toolkit/cactus   v2.9.3    6edb410ba0e5   3 months ago   1.03GB
broadinstitute/gatk                           4.1.3.0   0ef3d00baa09   5 years ago    3.72GB

Starting a container

When you start a docker container out of a docker image, you will have an isolated environment that is separated from the host, this is by design. In some cases though, you will want to use some data from the host (i.e. FASTQ files). You can start a container and at the same time attach a local folder to the container with the following code:

Terminal

docker run -it -v full_path_of_the_folder_within_host:mount_point_within_the_container docker_image_of_interest

-it: the container is started with the interactive mode so you can work within it
-v: used to mount/bind a folder from the host to the container

Moreover, you might want to use the -u option to specify the user that will be used to run the container. This will be handy if new files/folders are created within the container and you want to be able to access them from the host.

Terminal

docker run -it -v full_path_of_the_folder_within_host:mount_point_within_the_container docker_image_of_interest -u $(id -u):$(id -g)

<(...) is a bash command substitution and is preferred to use the output of one command, the command within the parentheses, in another command. In the example above, $(id -u) will be replaced by the user id of the user running the command docker run command and $(id -g) will be replaced by the group id of the user running the docker run command.

All in all, the easiest is to navigate to the folder of interest in your host machine and run the docker run ... command from within there:

Terminal

docker run -it -v ./:/data/ quay.io/comparative-genomics-toolkit/cactus:v2.9.3 -u $(id -u):$(id -g)

Do not forget to specify the TAG at the end.