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biobox minimal base image

About

This is contains a minimal debian base image for creating bioboxes. This bundles software which can make the verification and argument parsing steps of running a biobox easier. The included software are:

  • validate_inputs.sh - used to ensure the biobox.yaml given to the container is correct. This is run as the ENTRYPOINT directive in the Dockerfile. After checking the biobox.yaml file the script named by the BIOBOX_EXEC environment variable in the developer's Dockfile is called.

  • fetch_archive.sh - Given a URL and a name, fetches the URL and decompresses it to a directory under /usr/local with the given name.

  • biobox_args.sh - Fetches the biobox.yaml arguments and then applies a given jq path. An example of fetching fastq paths is:

    biobox_args.sh 'select(has("fasta")) | .fasta | map(.value)'

Using

Developing bioboxes using the bioboxes minimal base image requires creating a executable script inside the image and setting the environment variable BIOBOX_EXEC. This script will be executed by the validate_inputs.sh script after checking the biobox.yaml file is valid. The follow environment variables will also be set and are recommended to be used:

  • INPUT The location of the biobox.yaml file mounted in the container.
  • OUTPUT The location of the output directory where generated files should be placed, including a new biobox.yaml describing the generated outputs.
  • METADATA A directory for storing logs and other metadata.