Bioboxes Assembler Validator

This validator tool is provided to help developers ensure that their short read assembler biobox matches the specification. You can run the validator image to test your biobox image, and the output should help you identify any mismatches between your biobox and the specification.

Example usage

The use case for the validator is when you have created an assembler biobox and you would like to ensure it matches the biobox specification. The reason for doing this is that if your assembler is a valid biobox then anyone already using biobox assemblers in their bioinformatics pipeline can immediately start using yours. This is because all bioboxes interface are the same which allows for simple swapping and replacement of bioformatics tools.

# Fetch the latest 0.4.x release of the validator
tar xzf validate-short-read-assembler.tar.gz

./validate-short-read-assembler/validate bioboxes/velvet default

This example illustrates using the assembler validator to test the default task of the bioboxes/velvet image. The name of the assembler image and the task to are given as arguments to the validate script. If you would like to test your own image you only need to replace bioboxes/velvet with the name of the biobox image you are building.

How the validator works

All the commands and data are needed to test the image are included in inside the validator package. As long as you can successfully build your image first, the validator will run a series of scenarios simulating different user behaviour. The validator then ensures the container gives the expected response to each. These scenarios include missing FASTQ files, bad input data, and all the correct data to produce an assembly.