Some more documentation and Dockerfile

Dockerfile

+FROM ubuntu:20.04
+
+LABEL maintainer="Mustafa Tekpinar <tekpinar@buffalo.edu>"
+LABEL description="ESGEMME: Evolutionary and Structural Global Epistatic Model for Predicting Mutational Effects."
+
+WORKDIR /home/tekpinar/research/lcqb
+ENV JET2_PATH=/home/tekpinar/research/lcqb/JET2
+ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
+COPY ./JET2/ ./JET2/
+COPY ./naccess2.1.1 ./naccess2.1.1
+COPY ./ESGEMME/esgemme.py ./ESGEMME/esgemme.py
+COPY ./ESGEMME/pred.R ./ESGEMME/pred.R
+COPY ./ESGEMME/computePred.R ./ESGEMME/computePred.R
+COPY ./ESGEMME/default.conf ./ESGEMME/default.conf
+COPY ./ESGEMME/data/ ./ESGEMME/data/
+
+###################################################################
+RUN apt-get update --fix-missing && \
+apt-get install -y --no-install-recommends apt-utils &&\
+apt-get install -y software-properties-common && \
+apt-get install -y build-essential && \
+apt-get install -y python3-dev && \
+apt-get install -y python3-pip && \
+apt-get install -y r-base r-base-core && \
+apt-get install -y muscle && \
+apt-get install -y dssp && \
+apt-get install -y default-jre && \
+apt-get install csh && \
+apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+###################################################################
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN pip3 install --no-cache-dir prody matplotlib scipy pandas biotite
+RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
+
+
+

README.md

+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
 # ESGEMME: Evolutionary and Structural Global Epistatic Model for Mutational Effects                                                                                                             
 
-## 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.
+## Introduction
+ESGEMME is a program predicting mutational effects of a protein based on evolutionary and structural information.
+It can calculate effects of single point mutations and multiple point mutations.  
+We recommend using ESGEMME via our web site or our docker image. 
 
-### Installation from the source:
-
-#### 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/
-
-#### Installing the dependencies:
-ESGEMME has the following external dependencies:
-* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/
-* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
-These tools should be installed to be able to use ESGEMME.
 
 
-## Usage
-### Required input files
+## Input Data Requirements
 
 ESGEMME requires two files:
 * a multiple sequence alignment (MSA) file in fasta format (mandatory):
@@ -26,13 +18,26 @@ ESGEMME requires two files:
 
 * a structure file in PDB format (optional but recommended)
 
-Run the program by typing "python $ESGEMME_PATH/esgemme.py inputAli.fasta --pdbfile input.pdb ".
-A help can be accessed by typing "python $ESGEMME_PATH/esgemme.py --help".
+One of the fastest ways to obtain both input MSA and a PDB file is to run colabfold:
+https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
 
+Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in ESGEMME. 
 
+For testing purpose, you can find example input files for BLAT protein in data/ folder of this repository. 
+
+## Usage
 ### Running the program
 Let's assume that our input MSA is inputAli.fasta and input.pdb is our structure file in PDB format.   
 
+Run the program by issuing the following command in a bash terminal:
+```bash
+python $ESGEMME_PATH/esgemme.py inputAli.fasta --pdbfile input.pdb 
+```
+
+A quick help can be accessed by typing 
+```bash
+python $ESGEMME_PATH/esgemme.py --help
+```
 
 By default, GEMME will predict the effect of all possible single mutations at all positions in the 
 query sequence. Alternatively, a set of single or multiple mutations can be given with the option -m.
@@ -48,20 +53,43 @@ JET is run in its iterative mode, iJET, 10 times and the final conservation leve
 values obtained over the 10 iterations. 
 JET2 configuration file is: default.conf.
 JET2 output file is: myProt_jet.res.
-
-By default, GEMME will output mutational effects predictions obtained from the global epistatic model,
-the independent model, and a combination of those two using a reduced alphabet (alphabets/lw-i.11.txt):
-myProt_pred_evolEpi.txt
-myProt_normPred_evolEpi.txt
-myProt_pred_evolInd.txt
-myProt_normPred_evolInd.txt
-myProt_normPred_evolCombi.txt
+### Analyzing the ESGEMME output
+By default, ESGEMME will output the following files: 
+* myProt_pred_evolEpi.txt
+* myProt_normPred_evolEpi.txt
+* myProt_pred_evolInd.txt
+* myProt_normPred_evolInd.txt
+* myProt_normPred_evolCombi.txt
+
+The most important output file is **myProt_normPred_evolCombi.txt**. 
 The values of interest are the normalized predictions (normPred). Each file contains a 20 x n matrix, 
 where n is the number of positions in the query sequence.
 If the user provides her/his own list of mutations, then only the global epistatic model will be run 
 and the output file will contain 2 columns, the first one with the mutations, the second one with the 
 normalized predicted effects.
 
+## 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.
+
+### Installation from the source:
+
+#### 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/
+
+```bash
+export ESGEMME_PATH=/path-to-ESGEMME-directory/
+```
+
+#### Installing the dependencies:
+ESGEMME has the following external dependencies:
+* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/
+* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
+* naccess: http://www.bioinf.manchester.ac.uk/naccess/
+
+These tools should be installed to be able to use ESGEMME.
+
+
 # Cite 
 Laine E, Karami Y, Carbone A. GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects. Molecular Biology and Evolution, Volume 36, Issue 11, November 2019, Pages 2604–2619