Installation

Installation of Binette

Binette can be esailly installed with conda

conda create -c bioconda -c defaults -c conda-forge -n binette binette
conda activate binette

Binette should be able to run :

binette -h

Tip

For quicker installation and potential resolution of conflicting dependencies, consider using Mamba, an efficient alternative to conda.

A straightforward method to install Binette from the source code is by utilizing a conda environment that includes all the necessary dependencies.

1. Clone the Binette Repository

git clone https://github.com/genotoul-bioinfo/Binette
cd Binette

2. Installing Dependencies with a Conda Environment File

Install Binette dependencies listed in the binette.yaml file located at the root of the repository, using conda:

conda env create -n binette -f binette.yaml
conda activate binette

3. Installing Binette

Finally, install Binette using pip:

pip install .

Binette should be able to run :

binette -h

Binette is available on PyPI and can be installed using pip as follows:

pip install binette

In addition to Python dependencies, Binette requires a few external tools:

DIAMOND must be installed and available in your system’s PATH.
CheckM2 (version 1.1.0) is also required but not distributed on PyPI. You can install it directly from GitHub:

pip install git+https://github.com/chklovski/CheckM2.git@1.1.0

Before using Binette, it is necessary to download the CheckM2 database:

checkm2 database --download --path <checkm2/database/>

Make sure to replace <checkm2/database/> with the desired path where you want to store the CheckM2 database.