Updated Dockerfile for v1.4.0

Dockerfile

@@ -6,10 +6,11 @@ LABEL description="ESGEMME: Evolutionary and Structural Global Epistatic Model f
 ENV DEBIAN_FRONTEND=noninteractive
 
 WORKDIR /home/tekpinar/research/lcqb
-ENV JET2_PATH=/home/tekpinar/research/lcqb/JET2
+ENV JET2_PATH=/usr/local/JET2
 ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
-COPY ./JET2/ ./JET2/
-COPY ./naccess2.1.1 ./naccess2.1.1
+COPY ./JET2/ /usr/local/JET2
+COPY ./naccess2.1.1 /usr/local/naccess2.1.1
+
 COPY ./ESGEMME/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py
 COPY ./ESGEMME/esgemme/alphabets ./ESGEMME/esgemme/alphabets
 COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py
@@ -44,6 +45,13 @@ apt-get install -y hmmer && \
 apt-get install -y libboost-all-dev && \
 apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ###################################################################
+
+#Install naccess2.1.1
+WORKDIR /usr/local/naccess2.1.1
+RUN csh install.scr
+
+WORKDIR /home/tekpinar/research/lcqb
+
 #Install dssp v.3 because v.4 has some incompatibilites with biotite.
 RUN wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip
 RUN unzip -o master.zip 
@@ -67,7 +75,9 @@ ENV PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/
 RUN rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
 
 WORKDIR /home/tekpinar/research/lcqb
-RUN pip3 install -e ./ESGEMME/
+RUN sed -i s#/home/tekpinar/research/lcqb/JET2/matrix#/usr/local/JET2/matrix#g ./ESGEMME/esgemme/default.conf
+RUN sed -i s#/home/tekpinar/research/lcqb/naccess2.1.1/naccess#/usr/local/naccess2.1.1/naccess#g ./ESGEMME/esgemme/default.conf
+RUN pip3 install ./ESGEMME/
 RUN pip3 install -e ./demust/
 
 RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
@@ -86,15 +96,21 @@ RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.z
 
 # If run command on M1 Mac with macOS Monterey, you can remove sudo
 # Build command
-# sudo docker build -t tekpinar/esgemme-docker:v1.3.0 .
+# sudo docker build -t tekpinar/esgemme-docker:v1.4.0 .
 # sudo docker login
-# sudo docker push tekpinar/esgemme-docker:v1.3.0 
+# sudo docker push tekpinar/esgemme-docker:v1.4.0 
 
 # Pull command on M1 Mac with macOS Monterey
-# sudo docker pull tekpinar/esgemme-docker:v1.3.0
+# sudo docker pull tekpinar/esgemme-docker:v1.4.0
 
 # Run commands
-# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.3.0 /bin/bash
+# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.4.0 /bin/bash
+
+# Bind your current folder to a particular folder in docker.
+# In this way, you fall into the bash terminal of the docker image. 
+# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/esgemme-docker:v1.4.0
+
+#If you want to use the docker image like an executable file:
+# Please note that you must have aliBLAT.fasta and blat-af2.pdb inside your current folder and run this command!
+# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/esgemme-docker:v1.4.0 esgemme aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile  blat-af2.pdb
 
-# Bind your current folder to a particular folder in docker. 
-# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0