# Installation

ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME has many dependencies, we recommend using our web site or our docker image. If you are a determined user, here comes the steps required to install it from the source.

## Installing the dependencies:

ESGEMME has the following external dependencies:

- Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:

  - java

  - naccess: http://www.bioinf.manchester.ac.uk/naccess/

  - muscle: https://www.drive5.com/muscle/

- seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html

- dssp for secondary structure prediction.

These tools should be installed to be able to use ESGEMME.

## Getting the source code and preparing the environment:

Download the ESGEMME source code from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME. Define and export the environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/

    export ESGEMME_PATH=/path-to-ESGEMME-directory/

## Configuring default.conf file

Inside ESGEMME folder, there is an important file called default.conf. This file contains essential parameters of ESGEMME, such as paths of external parts, default internal parameters. etc. You have to correct the Software section of this file according to your system.