We have to sometimes prepare custom images to meet our needs either by building a new image from Dockerfile or adding missing software tools on pre-built images. And also, we usually want to re-use the customised image later by ourselves or share it with other collaborators. One way to share images with others is to use image registries such as DockerHub! In this session, you will learn to modify existing Docker image and share it with others via DockerHub. For this purpose, we will make use of FastQC software image from DockerHub as a starting image for modification.
This exercise requires a workstation with docker client installed and thus can’t be done in CSC HPC environment. Use PWD terminal instead.
Deploy FastQC Container
Let’s launch FastQC container interactively as it is easy for testing or development. For that, use docker run command with special flag -it so that the command attaches you with an interactive terminal inside the container as shown below:
docker container run -it biocontainers/fastqc:v0.11.9_cv7 /bin/sh
Note: the flags -it are short for -i -t which are the short forms of –interactive (Keep STDIN open) and –tty (allocate a terminal).
Modify FastQC Container
Now that you are inside the container, you can modify the image as you wish. Just for illustration, as FastQC container lacks vim editor, you can install vim inside the container as shown below:
apt-get update && apt-get install -y vim
use Ctrl + p then Ctrl + q on terminal to detach from container.
Commit the modified changes to FastQC image
Let’s find out the container id corresponding to the FastQC container into which you have installed vim editor using docker ps -a command on the
terminal. Once we have container id, you are ready to commit the changes as shown below:
docker ps -a
docker commit <container id> fastqc-vim:test # docker commit 6527b0394bdf fastqc-vim:test
Push your image to your DockerHub repository
Sharing an image via docker registry such as DockerHub (the most popular image registry, hosting hundreds of thousands of images) is an efficient way of sharing and managing your images. Once an image is in a docker (public) registry, anyone can pull it from there. However, this involves setting up an account in DockerHub. If you don’t have DockerHub account already, here are few steps you can do to set-up your account:
Once you have docker credentials in place, you are ready to push the image. But before pushing your docker image to DockerHub, you just need to rename docker image
to your namespace/account first using docker tag command as below:
docker tag <image id> your-dockerhub-user-name/repo-name[:tag] # find <image id> corresponding to repository, fastqc-vim by typing `docker images` command
on host machine. e.g., command: docker tag f689b999263b your-dockerhub-user-name/fastqc-vim:test
All images should be tagged with an appropriate prefix to repository name before pushing an image.
Push your image finally as below:
docker login # authenticate yourself using DockerHub credentials
docker push your-dockerhub-user-name/repo-name[:tag] # docker push your-dockerhub-user-name/fastqc-vim:test
Once the push to repository is successful, your image is now available for everyone to use. Go to your profile page on the DockerHub to view your new docker image.