wdl-dockerfiles

This repo houses definitions for the Docker images used by PacBio workflows.

Directory structure

Docker image definitions are found in the docker directory.

Each Docker image must minimally define a build.env file.

Example directory structure:

docker/
├── bwa_mem/
│   ├── build.env
│   └── Dockerfile
├── Conda_dockerfile # a template dockerfile, used to build multiple images
├── htslib/
│   └── build.env # Uses the Conda_dockerfile
├── pb_human_wgs_scripts/
│   ├── build.env
│   └── Dockerfile
├── samtools/
│   ├── build.env
│   ├── Dockerfile
│   └── scripts/
└── yak
    └── build.env # Uses the Conda_dockerfile

The build.env file

Each target image is defined via the presence of a build.env file, which is used to specify the name and version tag for the corresponding Docker image. It must contain at minimum the following variables:

• IMAGE_NAME
• IMAGE_TAG

All variables defined in the build.env file will be made available as build arguments during Docker image build.

The IMAGE_TAG variable can be built using other variables defined in the build.env file, as long as those other variables are defined before IMAGE_TAG. For example, the following IMAGE_TAG would be set to 0.7.8_1.15:

# Tool verisons
BWA_VERSION=0.7.8
SAMTOOLS_VERSION=1.15

# Image info
IMAGE_NAME=bwa_samtools
IMAGE_TAG=${BWA_VERSION}_${SAMTOOLS_VERSION}

The Dockerfile corresponding to a build.env must either:

1. Be named Dockerfile and exist in the same directory as the build.env file, or
2. Be specified using the DOCKERFILE variable in the build.env file (e.g. for image builds that reuse a common Dockerfile). The path to the Dockerfile should be relative to the directory containing the build.env file.

Special variables

These variables have special meanings when the Docker image is being built. † specifies that the variable is required.

• IMAGE_NAME†: specifies the name of the built image
• IMAGE_TAG†: specifies the tag of the built image
• NOBUILD: When set to true, skip building this image
• DOCKERFILE: Specify an alternate path to a Dockerfile, relative to the build.env file. If left undefined, the Dockerfile must be named Dockerfile and be present at the same directory level as the corresponding build.env file.
• CONDA_ENVIRONMENT_TEMPLATE: For conda-based images, set this to the path (relative to the build.env file) to the conda environment template file. This file may have variables set in place of tool versions and will be populated with the variables from build.env at build time.

Building Docker images

Docker images can be built using the build_docker_images utility script.

Build a single image

./util/build_docker_images -d docker/smrtcell_stats

Build all images in the docker directory

./util/build_docker_images -d docker

Build and push all images in the docker directory

./util/build_docker_images -d docker -p

Build and push all images in the docker directory, using the pacbio container registry

./util/build_docker_images -d docker -p -c pacbio