Base and R2DT Docker Images


This project uses a combination of two Docker images: base_image and the R2DT image. The base_image contains all non-Python dependencies of R2DT, while the R2DT image includes the necessary Python packages.

Base Image

The build process for the base image is detailed in base_image/Dockerfile. It uses GCC to compile C/C++ code and installs additional dependencies, such as Perl-related tools.

Once built, the base image is uploaded to Docker Hub under the name rnacentral/r2dt-base.

Rebuilding the base image is rare and is necessary only when an R2DT dependency is updated and needs integration into the R2DT build.

View rnacentral/r2dt-base on Docker Hub →

R2DT Image

The R2DT image is constructed using the Dockerfile located in the repository’s root folder. It inherits from r2dt-base.

This approach ensures that the R2DT image remains compact, containing only the Python and R2DT dependencies, excluding the extensive build tools used in the base image. Most changes in the Python code can be made using the prebuilt dependencies and do not require recompilation of C/C++ code.

View rnacentral/r2dt on Docker Hub →

Upgrade Process

When updating the base image, follow these steps:

  1. Create a branch from develop and make necessary changes to base_image/Dockerfile.

  2. Build the base image locally and test it. Use the just bbuild command to build the base image locally and just full-build to build both the base image and the main image locally.

  3. Submit a pull request, triggering image build via GitHub Actions. The resulting base image will be tagged with your pull request ID (e.g., rnacentral/r2dt-base:pr-109).

  4. If you plan to use the newly built image in subsequent R2DT development, notify the repository maintainers. Ask them to tag your image as a new release version using the corresponding workflow. Only repository maintainers have permission to run this workflow. Update the FROM directive in the R2DT’s image Dockerfile to reference the newly tagged base image.

Note: If you would like to build the R2DT image against a custom version of the base image, you can do so by using just tag-build <TAG> command:

# build r2dt image against the base image tagged as pr-109
just tag-build pr-109

# build r2dt image against the base image tagged as latest
just tag-build latest

Note: When changes to both base and R2DT images are required, it is recommended to submit separate pull requests. This allows the base image to be built with the new version on Dockerhub before the R2DT image is built with the updated base image.

Building for non-default platforms/architectures

Should you need to build any of the images for a different platform (e.g., arm64), you can do so by specifying the platform=PLATFORM_NAME flag when building the image. For example:

# build base image for linux/arm64
just platform=linux/arm64 bbuild

# build r2dt image for linux/amd64
just platform=linux/amd64 build

# build both images for darwin/arm64
just platform=darwin/arm64 full-build