Bioboxes command line interface

The command line interface (CLI) allows you to use the biobox pre-packaged bioinformatics tools in your research and workflows without having to understand Docker. The CLI allows you to run a biobox, giving it your input data files and then getting the generated output files.

Quick Start

# Install the CLI
pip install --user biobox_cli

# Assemble paired fastq reads into contigs
biobox run \
  short_read_assembler \
  bioboxes/megahit \
  -i YOUR_READS.fq.gz \
  -o contigs.fa


The CLI requires Docker and python/pip to installed on your system. These are the only required dependencies, all other dependencies are included in each biobox. You may install Docker using the Docker toolbox. Instructions are available for installing or upgrading pip. Once you have Docker and pip installed you can install the biobox CLI as follows:

pip install --user biobox_cli

Using a biobox

The reason to use bioboxes is that they allow you to access many different bioinformatics software tools, but without the often associated pain of installing or getting to learn the interface. Once installed, the biobox CLI allows you to use biobox tools on your data to get the results you want. The general CLI is as follows:

# The general interface
biobox run <box_type> <container> [options]

The <box_type> argument specifies what type of biobox you would like to use, e.g. short_read_assembler. These are the bioboxes used to assemble short Illumina reads from a genome into contigs.

The second argument <container> is the specific biobox you would like to use. A list of different available bioboxes can be found on the "Biobox Images" section of this site. An example of using the biobox CLI to run the megahit genome assembler on gzipped paired reads is as follows:

# An example using megahit for genome assembly
biobox run \
  short_read_assembler \
  bioboxes/megahit \
  --input reads.fq.gz \
  --output contigs.fa

You can get further information on how to use the biobox CLI using the --help flag.

# Get help output on using the CLI
biobox --help