# 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.

## Preparation of the environment and installation of ESGEMME

Step by step installation on Ubuntu 22.04

Prepare your environment and install the required packages:

    sudo apt-get update --fix-missing && \
    sudo apt-get install -y --no-install-recommends apt-utils && \
    sudo apt-get install -y software-properties-common && \
    sudo apt-get install -y autotools-dev && \
    sudo apt-get install -y automake && \
    sudo apt-get install -y build-essential && \
    sudo apt-get install -y python3-dev && \
    sudo apt-get install -y python3-pip && \
    sudo apt-get install -y r-base r-base-core && \
    sudo apt-get install -y muscle && \
    sudo apt-get install -y default-jre && \
    sudo apt-get install -y ncbi-blast+ && \
    sudo apt-get install -y nano && \
    sudo apt-get install -y less && \
    sudo apt-get install -y wget && \
    sudo apt-get install csh && \
    sudo apt-get install -y hmmer && \
    sudo apt-get install -y libboost-all-dev && \
    sudo apt-get clean && \
    sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

#Dssp installation If you are using Ubuntu 20.04, you can install dssp by the following command .. code:: bash

> sudo apt-get install dssp

Otherwise, you can install it from the source by the following commands. Please note that default dssp in Ubuntu 22.04 is not working properly. .. code:: bash

> wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && unzip -o master.zip && cd dssp-master/ && ./autogen.sh && ./configure && make && sudo make install && sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp && cd ../ && sudo rm -rf dssp-master/ && sudo rm -f master.zip

#HHSUITE installation .. code:: bash

> wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && mkdir hhsuite && mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ && cd hhsuite && tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz && rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz

#Add it to your path permanently inside .bashrc or .profile or .bash_profile Check the location of hhsuite folder and add it to your path In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line to my .profile file. PATH=”/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH”

Then source ~/.profile

#

> cd ESGEMME

#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.! .. code:: bash

> cd ESGEMME

## Configuring default.conf file

Inside ESGEMME/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.

    pip3 install -e . &&\
    cd ../

#Installing the required R packages .. code:: bash

> sudo Rscript -e ‘install.packages(“seqinr”, repos=”http://cran.us.r-project.org”, dependencies=TRUE)’

#Installing secondary programs such as ev_couplings to obtain MSA files.

    wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip && \
    unzip -o master.zip && \
    cd plmc-master && \
    make all-openmp32 && \
    sudo cp bin/plmc /usr/local/bin/ && \
    cd ../ && \
    rm -rf master.zip plmc-master