Using Docker or Podman for Containerizing Code

We will containerize all packages which can be redistributed without licenses using Docker containers. You can work with these using either Docker or Podman.

Creating a New Dockerfile and Docker Image

Create a local Dockerfile that loads/installs necessary packages (and their versions) necessary to run the code in the Github repo.

How to create a docker registry in CAVATICA

Create a repository

  • Log into CAVATICA using one of the lab accounts. CAVATICA logins for Children's BTI and Rokita Lab are pinned to #rokita-lab-internal slack channel.
  • Click on Developer tab -> Docker registry
  • Click + Create repository (top right)
  • Type repository name and choose visibility and click create.

create-new-repo

  • Assign admin rights to Jo Lynne Rokita (harenzaj) and Alex Sickler (sicklera) by clicking on: <Name of Repository>/ Members
  • Assign admin rights to yourself so that you can push the image once it's built

Docker Login

From the directory where your Dockerfile lives, log into CAVATICA docker registry using your CAVATICA credentials. 

docker login http://pgc-images.sbgenomics.com/ -u <USERNAME> -p <YOUR-AUTH-TOKEN>

"USERNAME" refers to your CAVATICA username. "YOUR-AUTH-TOKEN" can be generated from your CAVATICA account under the “Authentication token” section in the Developer tab.

Build Image

docker build -t pgc-images.sbgenomics.com/<username>/<repository_name>[:tag] .

Example: 

docker build -t pgc-images.sbgenomics.com/naqvia/autopvs1:latest .

For Mac users with Apple silicon chips (M1-M4 chip), you may need to specify the platform

docker build --platform=linux/amd64 -t pgc-images.sbgenomics.com/<username>/<repository_name>[:tag] .

Example: 

docker build --platform=linux/amd64 -t  pgc-images.sbgenomics.com/naqvia/autopvs1:latest .

Push the Docker Image

docker push pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

where <username>/<repository_name>[:tag] refers to the image that you have already committed

Example: docker push pgc-images.sbgenomics.com/naqvia/autopvs1:latest

Pulling the Docker Image

docker pull pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]:<tagname>

Example: 

docker pull pgc-images.sbgenomics.com/naqvia/autopvs1:latest

Updating the Docker Image

Make any necessary changes to Dockerfile and run docker build as done previously.

Example: 

docker build --platform=linux/amd64 -t pgc-images.sbgenomics.com/<username>/<repository_name>:latest .

Here, "username" should match the namespace used in the existing Docker container. For example, it should be "rokita-lab", not your personal CAVATICA username, in the repository below.

Once complete, the output will print Successfully built <image ID>. Tag this image ID to the remote repo and push using these steps: 

docker tag <image ID> pgc-images.sbgenomics.com/<username>/<repository_name>:[tag]
docker push pgc-images.sbgenomics.com/<username>/<repository_name>:[tag]

For more, please review the full documentation.

For more about Docker using M1/M2/M3 chip macs, (see here).