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: - 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/

.. code:: bash

   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.