README.md

bioinformatics-public-docker-images

This repository contains public docker images used for workflow execution.

DNAstack's public images built from the files in this repository are hosted on Dockerhub.

Directory structure

Each tool or set of tools should have its own directory containing at minimum a build.env file. If docker definitions for multiple versions of the same tool exist (e.g. samtools version 0.19 and version 1.15), they can be further divided into subdirectories within the samtools directory, named by the tool version.

See the build script documentation for more information on the build.env file and how images can be named and tagged.

See image naming and versioning for information on how images should be named and versioned.

Example directory structure:

bioinformatics-public-docker-images
└── docker
    ├── bcftools_r
    │   ├── build.env
    │   └── Dockerfile
    ├── bwa_samtools
    │   ├── build.env
    │   └── Dockerfile
    ├── samtools
    │   ├── 0.19
    │   │   ├── build.env
    │   │   └── Dockerfile
    │   └── 1.15
    │       ├── build.env
    │       └── Dockerfile
...
    ├── toolA
    │   ├── build.env
    │   └── Dockerfile
    └── toolA_toolB
        ├── build.env
        └── Dockerfile

Image naming and versioning

Images should be named and versioned using this flowchart:

General best practices

• The Dockerfile should always be named Dockerfile
• Do not write secrets into docker images; if secrets are needed as part of workflow execution, they should be provided as workflow inputs
• Avoid adding large reference files to docker images where possible; provide as workflow inputs
• Do not use the latest tag unless you really need things to update automatically; this is prone to breaking
• OS repos and versions of tools in these repos change; prioritize installing tools directly from source
• Make all tool versions environment variables (e.g. ENV BCFTOOLS_VERSION 1.15.1) that are controlled within the build.env file
• The Dockerfile should ideally consume all build arguments defined in the build.env file, e.g. by setting them as image environment variables