1. Installation

Installation Guide for RepGenR

This guide will walk you through the setup process for RepGenR. To ensure a smooth installation, RepGenR has a number of dependencies that need to be installed.

Prerequisites

Before proceeding with the installation of RepGenR, make sure that you have Python 3 installed on your system. The following external libraries and software are required:

• dRep
• CheckM
• NCBI Datasets CLI
• MashTree
• ProgressiveMauve
• IQ-TREE
• ETE Toolkit (ETE3)
• Matplotlib

All these dependencies are available through Conda, using the Bioconda channel.

Installation Steps

Follow these steps to create an environment for RepGenR and install all the required dependencies:

Step 1: Create Environment and Install Dependencies

We recommend using mamba, a fast and reliable alternative to conda. If you don't have mamba installed, you can install it via conda:

conda install mamba -n base -c conda-forge

Create a new environment named RepGenR and install all dependencies:

mamba create -n RepGenR -c bioconda -y python=3 matplotlib requests drep checkm-genome ncbi-datasets-cli mashtree progressivemauve iqtree ete3

Step 2: Clone the RepGenR Repository

Clone the RepGenR repository from GitHub:

git clone https://github.com/FOI-Bioinformatics/repgenr.git

Step 3: Install RepGenR

Activate the newly created RepGenR environment:

conda activate RepGenR

Navigate to the cloned repository directory and install RepGenR using pip:

cd repgenr
pip install .

Post-installation Check

After installation, it's good practice to verify that RepGenR is properly installed. Run the following command:

repgenr --version

If you see the version number of RepGenR output to the terminal, the installation was successful.

Troubleshooting

Should you encounter any issues during the installation, please refer to the following resources:

• RepGenR Issues Page for known issues and their solutions.
• Bioconda Documentation for troubleshooting Conda-related issues.

For further assistance, don't hesitate to contact the RepGenR developers or file an issue on GitHub.