/how_to_use_docker

Installing docker

If using ubuntu and apt-get:

sudo apt update

sudo apt install docker.io

For Fedora or CentOS, change apt to yum or dnf, depending on which one you use.

Post-installation setup

https://docs.docker.com/engine/install/linux-postinstall/

Test in a clean version of ubuntu in the interactive mode

docker run -it ubuntu:latest

Mount a local folder inside the docker with writing access

docker run -v /home/tsantini/my_folder_at_host:/mnt/myfolder -it name_of_container:latest

Build a new conteiner

docker build -t name_of_the_conteiner folder_with_Docker_file

Example of Docker file

It has to be saved with the name Dockerfile inside the folder_with_Docker_file

FROM ubuntu:latest
RUN apt update && \
    DEBIAN_FRONTEND=noninteractive \
    apt install -y --no-install-recommends \
    vim \
    git \
    g++ \
    gcc \
    tmux \
    ca-certificates \
    make \
    cmake-curses-gui \
    file \
    dc \
    libpthread-stubs0-dev \
    parallel

Mount a local folder inside the docker with writing access

After building and testing your container, you might be interested in communicating your container with the host to share files. Please type the following:

docker run -v /home/tsantini/my_folder:/mnt/myfolder -it container_name:latest

Running the image_processing container (available at dockerhub)

This container has several MRI image processing packages.

docker run -v local_folder:mounting_folder --rm -it tsantini/image_processing

To test, you can run:

mrconvert --help

More information about this conteiner at https://hub.docker.com/r/tsantini/image_processing

You can request access to the Dockerfile for this conteiner.

Useful flags

-it interactive mode: open the container as a terminal

-v host_location:docker_mount_location mount a local folder into the docker, for example: -v /home/tsantini/my_folder:/mnt/myfolder

--rm remove the content of the conteiner after exiting. It's usually the default.

Running the container as host user

Add the following argument to docker run:

-u $(id -u ${USER}):$(id -g ${USER})

Pushing container to Docker Hub

  1. Login to docker hub

docker login --username=your_user_name

  1. check the image you want to push

docker images

  1. tag this image

docker tag image_ID your_user_name/image_name:new_tag

  1. push the container

docker push your_user_name/image_name

Reflaging a container

  1. check the images

docker images

  1. retag

docker tag images_ID your_user_name/image_name:new_tag

removing flag

docker rmi image_name:flag

saving and loading containers

docker save [OPTIONS] IMAGE [IMAGE...] -> saves the conteiner in a tar file, for example docker your_user_name/image_name > ~/conteiner.tar

docker load [OPTIONS] -> loads the conteiner from a tar file, for example docker load < ~/conteiner.tar

saving a docker conteiner as singularity format

example:

singularity pull camino.sif docker://tsantini/camino:latest

example how to run singularity sif container:

singularity exec -B $PWD:$PWD -W $PWD ./container.sif commands_inside_container

checking the stats of the conteiners

docker ps -> check the running conteiners

docker stats -> shows the CPU/memory/IO usage of the conteiners

commiting changes

docker ps -> check the running conteiners

docker commit container_ID your_user_name/image_name:tag -> commit the container

docker push your_user_name/image_name:tag -> push to dockerhub

How to use docker on windows with wsl without the docker app

  • enable anyone in docker group to run dockerd without password
  1. in the wsl2 terminal, type sudo visudo
  2. add this lines to the file: %docker ALL=(ALL:ALL) NOPASSWD: /usr/bin/dockerd
  • write a script to check if the dockerd is already runing, if not, start it
#!/usr/bin/bash
if ! docker info > /dev/null 2>&1; then
  echo "This script uses docker, starting it now"
  sudo dockerd > ~/dockerd.txt 2>~/dockerd_err.txt &
fi

  • add the script to your .bashrc, example: /home/username/start_docker.sh

  • go to your .docker\config.json and remove the line that starts with credsStore, you will be able to login in your dockerhub after that

Cleaning up

Delete some images:

docker rmi id:tag
docker image prune -f

Delete all containers using the following command:

docker rm -f $(docker ps -a -q)

Delete all volumes using the following command:

docker volume rm $(docker volume ls -q)

Clean up unused stuff:

docker container prune -f
docker image prune -f
docker volume prune -f