Installation

Pre-requisites

CoCoNet was tested on both MacOS and Ubuntu 18.04. To install and run CoCoNet, you will need:

1. python (>=3.5, recommended: 3.7)
2. pip3, the python package manager or the conda installer.

If you encounter any issue during the installation, you should retry in a fresh environment (with conda or virtualenv) with the recommended python version (3.7).

Install the latest release on PyPi

You can install CoCoNet, from the Python Package Index. To install it, you simply need to run the following command (you can omit –user if you’re working in a virtual environment).

# Install numpy until scikit-bio issue #1690 is resolved
pip install --user numpy
# Install CoCoNet
pip3 install --user coconet-binning

Install the development version

You can also install the most up to date version with the following command:

# Install numpy until scikit-bio issue #1690 is resolved
pip install --user numpy
# Install CoCoNet
git clone https://github.com/Puumanamana/CoCoNet.git && cd CoCoNet
pip install --user .

If you encounter any issue with the development version, you should try with the latest release as the development version might not have been thoroughly checked.

Install with bioconda

CoCoNet is available in bioconda. You will need miniconda or anaconda installed on your computer. CoCoNet can be installed using the following command:

# Install in a new environment
conda create -n coconet -c bioconda -c conda-forge coconet-binning
# Switch environment
conda activate coconet

Using Docker

Alternatively, CoCoNet can be pulled directly from DockerHub. Assuming your contigs are located in /data/contigs.fasta and your indexed bam files are in /data/.bam and /data/.bai, then you can run CoCoNet with the following command:

docker run -v /data:/workspace nakor/coconet coconet run --fasta contigs.fasta --bam *.bam