Added evcouplings to the image for MSA generation.

.gitignore

@@ -4,5 +4,6 @@
 example/.RData
 gemmeAnal.pyc
 __pycache__/*
+esgemme/__pycache__/
 esgemme.egg-info/*
 .RData
\ No newline at end of file

Dockerfile

@@ -36,6 +36,7 @@ apt-get install -y nano && \
 apt-get install -y less && \
 apt-get install -y wget && \
 apt-get install csh && \
+apt-get install -y hmmer && \
 apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ###################################################################
 RUN wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz
@@ -55,6 +56,17 @@ RUN pip3 install -e ./demust/
 
 RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
 
+
+#PLMC and EVcouplings installation for obtaining sequences.
+RUN wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip
+RUN unzip master.zip
+WORKDIR /home/tekpinar/research/lcqb/plmc-master
+RUN make all-openmp32
+RUN cp bin/plmc /usr/local/bin/
+WORKDIR /home/tekpinar/research/lcqb
+RUN rm -r master.zip plmc-master
+RUN pip3 install install https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
+
 # Build command
 # sudo docker build -t tekpinar/esgemme-docker:v1.3.0 .
 # sudo docker login