2. Installation

Direct install

Before you can install Bactabolize you will need to make sure you have installed all of its dependencies and that they are available in your path.

You can then simply clone the Bactabolize repository, which will be ready to use.

git clone https://github.com/kelwyres/Bactabolize

Alternatively, you can use Conda environments to install Bactabolize and all of its dependencies simultaneously, as described below. We recommend mamba as a package installer as it is much faster.

Conda environment

The easiest way to install Bactabolize is via a Conda environment using the mamba package installer, as this will take care of all of the dependencies for you. Conda can be installed as described here.

# Install mamba in base conda
conda install -n base -y -c conda-forge mamba

# Create and activate environment via mamba
mamba create -n bactabolize -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.6'
conda activate bactabolize

# Test installation
bactabolize -h

Dependencies

Before you can install Bactabolize you will need to make sure you have installed all of its dependencies and that they are available in your path. Mamba will install these automatically. These are required IF you clone the repository.

• python ==3.9
• biopython 1.79
• glpk==5.0
• swiglpk==5.0.10
• urllib3=2.2.2
• cchardet==2.1.7
• tabulator=1.25.1
• goodtables==2.5.4
• openpyxl==2.4.11
• blast 2.16.0
• cobra 0.21.0
• prodigal 2.6.3
• memote 0.13.0