Installation

There are several ways to install Bin Chicken

System requirements

The purpose of Bin Chicken is to suggest sets of samples for coassembly. The coassembly process can use upwards of 250GB of RAM and 32 cores, so we recommend running on a HPC system if you intend to assemble and recover genomes.

Bin Chicken is supported for Linux (tested on SUSE 12.5). Specific dependencies are listed in binchicken.yml.

Install from Bioconda

Install latest release via bioconda.

conda create -n binchicken -c bioconda -c conda-forge binchicken

Install from pip

Install latest release via pip.

pip install binchicken

Install from source

Create conda env from binchicken.yml and install from source.

git clone https://github.com/AroneyS/binchicken.git
cd binchicken
conda env create -f binchicken.yml
conda activate binchicken
pip install -e .