Added reformat.pl script to the image.

Dockerfile

@@ -26,17 +26,28 @@ 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 hhsuite && \
 apt-get install -y default-jre && \
 apt-get install -y ncbi-blast+ && \
 apt-get install -y nano && \
 apt-get install -y less && \
+apt-get install -y wget && \
 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 wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz
+RUN mkdir hhsuite
+RUN mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/
+
+WORKDIR /home/tekpinar/research/lcqb/hhsuite
+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 ./demust/
 RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
 
@@ -51,3 +62,5 @@ RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org",
 # Run command on M1 Mac with macOS Monterey
 # docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.3.0 /bin/bash
 
+# 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