Small changes for docker installation.

I adapted my code and Dockerfile to accomodate
pip installable version of ESGEMME.

Dockerfile

@@ -8,7 +8,11 @@ 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/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py
+COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py
+COPY ./ESGEMME/setup.py ./ESGEMME/setup.py
+COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt
+COPY ./ESGEMME/README.md ./ESGEMME/README.md 
 COPY ./ESGEMME/pred.R ./ESGEMME/pred.R
 COPY ./ESGEMME/computePred.R ./ESGEMME/computePred.R
 COPY ./ESGEMME/default.conf ./ESGEMME/default.conf
@@ -43,12 +47,12 @@ RUN tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz
 ENV PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
 RUN rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
 
-
 RUN ln -s /usr/bin/python3 /usr/bin/python
-RUN pip3 install --no-cache-dir prody matplotlib scipy pandas biotite
 
 WORKDIR /home/tekpinar/research/lcqb
+RUN pip3 install -e ./ESGEMME/
 RUN pip3 install -e ./demust/
+
 RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
 
 # Build command

esgemme/esgemme.py

@@ -838,7 +838,7 @@ def parse_command_line():
         argparse parser.
     """
     parser = argparse.ArgumentParser(
-        prog="gemme",
+        prog="esgemme",
         description="""
             ESGEMME (Evolutionary and Structural Global Epistasis Model for predicting Mutational Effects) 
             is a tool to predict mutational outcomes based on sequence and structure analysis

requirements.txt

-numpy
+prody
+numpy<1.24,>=1.10
 matplotlib
 scipy
 pandas
-biopython
+biopython<=1.79
 biotite
-prody
+