0 Installation

The program is designed to have an easier installation procedure on UNIX-based machines, nonetheless the code is compatible with Windows systems as well.
(tested on: Ubuntu 20.04 LTS with Linux 5.13 kernel - Windows 10 build 19043.1526 - March 2022)

Windows systems can use the "Windows Subsystem for Linux" extra feature, as described here.

The easiest way to install KEMET using both UNIX or Windows subsystem is through the Anaconda package manager. You could see Anaconda documentation at this link.

Anaconda installation

A quick Anaconda installation is achieved with:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Create a new environment and install dependencies

With Anaconda properly set, it is possible to create an environment called "kemet" using

conda create --name kemet python=3.7
conda activate kemet

To install other dependencies use the following commands:

conda install -c bioconda mafft hmmer diamond prodigal
pip install reframed

# OPTIONAL (only if GSMM mode use is intended)

pip install carveme

Git repository installation

2. Clone the git repository in your preferred working directory, and access it.
   It's also possible to download a compressed version directly from this GitHub repository.

git clone https://github.com/Matteopaluh/KEMET.git && cd KEMET