biobox.yaml Validator

Biobox authors should check the input data provided by the user is valid before starting. This will prevent unexpected program behaviour or errors halfway through a multi-step pipeline. Any errors should be reported back to the user with a clear message so they can be understood and fixed.

The bioboxes project provides the command line tool validate-biobox-file to help test the input YAML file given to a biobox. This tool with test the YAML and return a non-zero exit code and error message if the biobox data is not correct. If identified, this error message should be returned to the user, and then the biobox should exit. The command line interface for this tool is:

validate-biobox-file --schema=schema.yml --input=input.yml

Download the latest version.

Example install

The tool validate-biobox-file can be installed in your Docker image by downloading and unpacking. An example is to fetch the latest major version release and decompress it into the directory /biobox-validator.

RUN mkdir /biobox-validator
RUN wget \
      --quiet \
      --output-document -\
      ${BASE_URL}/${VERSION}/validate-biobox-file.tar.xz \
    | tar xJf - \
      --directory /biobox-validator \

Example usage

The tools should be used at the start of a script to ensure the data passed by the user is correct. One way to do this is with a bash script that exits when a non-zero exit code is generated.


set -o errexit

/biobox-validator/validate-biobox-file \
  --schema=schema.yml \