Dockerfile

# FAVITES minimal docker image using Ubuntu base
FROM ubuntu:20.04
MAINTAINER Niema Moshiri <niemamoshiri@gmail.com>

# Set up environment
RUN apt-get update && apt-get -y upgrade && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y autoconf bison curl default-jre flex git gsl-bin libcurl4-openssl-dev libgsl0-dev libmodule-install-perl libncurses5-dev libncursesw5-dev libssl-dev libtool python3 python3-pip unzip wget zlib1g-dev
RUN mkdir -p /etc/perl/CPAN && echo -e "'urllist' => [\n    q[http://mirror.bhoovd.com/CPAN/],\n    q[http://cpan.develooper.com/],\n    q[http://cpan.cs.utah.edu/]\n]," >> /etc/perl/CPAN/Config.pm
RUN echo -e "y\nexit\n" | cpan && cpan App::cpanminus && cpanm --force Bio::Perl

# Set up Python 3 and modules
RUN pip3 install dendropy && \
    pip3 install treeswift && \
    pip3 install treesap && \
    pip3 install networkx && \
    pip3 install numpy && \
    pip3 install pandas && \
    pip3 install scipy && \
    pip3 install pyvolve

# Set up ART (MountRainier-2016-06-05)
RUN wget -O- "https://github.com/niemasd/FAVITES/blob/master/dependencies/artsrcmountrainier2016.06.05linux.tgz?raw=true" | tar xz && \
    cd art_src_MountRainier_Linux && make && mv art_* /usr/local/bin && cd .. && rm -rf art_src_MountRainier_Linux

# Set up DWGSIM
RUN git clone --recursive https://github.com/nh13/DWGSIM.git && \
    cd DWGSIM && make && mv dwgsim* /usr/local/bin && cd .. && rm -rf DWGSIM

# Set up GEMF
RUN git clone https://github.com/niemasd/GEMF.git && \
    cd GEMF && make && mv GEMF /usr/local/bin && cd .. && rm -rf GEMF

# Set up Grinder
RUN wget --no-check-certificate -qO- https://tenet.dl.sourceforge.net/project/biogrinder/biogrinder/Grinder-0.5.4/Grinder-0.5.4.tar.gz | tar -xz && \
    cd Grinder* && echo -e "y\n" | perl "Makefile.PL" && echo -e "yes\n" | make && make install && cd .. && rm -rf Grinder*

# Set up HMMER
RUN curl http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz | tar xz && \
    mv hmmer*/binaries/* /usr/local/bin && rm -rf hmmer*

# Set up Seq-Gen
RUN git clone https://github.com/rambaut/Seq-Gen.git && \
    cd Seq-Gen/source && make && mv seq-gen /usr/local/bin && cd ../.. && rm -rf Seq-Gen

# Set up Dual-Birth Simulator
RUN git clone https://github.com/niemasd/Dual-Birth-Simulator.git && \
    cd Dual-Birth-Simulator && make && mv dualbirth /usr/local/bin && mv yule /usr/local/bin && cd .. && rm -rf Dual-Birth-Simulator

# Set up Newick Utilities
RUN wget https://github.com/tjunier/newick_utils/archive/refs/heads/master.zip && \
    unzip master.zip && \
    cd newick_utils-master && \
    autoreconf -fi && \
    ./configure && \
    make && \
    make install && \
    cd .. && \
    rm -rf master.zip newick_utils-master

# Set up msms
RUN wget https://www.mabs.at/fileadmin/user_upload/p_mabs/msms3.2rc-b163.zip && unzip msms*.zip && \
    mv msms/lib/* /usr/local/lib && mv msms/bin/* /usr/local/bin && chmod a+x /usr/local/bin/msms && rm -rf msms*

# Set up SimPhy
RUN wget -O- "https://github.com/adamallo/SimPhy/releases/download/v1.0.2/SimPhy_1.0.2.tar.gz" | tar -zx && \
    mv SimPhy_1.0.2/bin/simphy_lnx64 /usr/local/bin/simphy && chmod a+x /usr/local/bin/simphy && \
    rm -rf *SimPhy* .*SimPhy*

# Set up FAVITES
RUN git clone https://github.com/niemasd/FAVITES.git
ENV PATH="/FAVITES:${PATH}"
ENV FAVITES_DOCKER=TRUE
RUN mkdir -p /FAVITES_MOUNT

# Clean up
RUN find /usr/lib/python3.*/ -name 'tests' -exec rm -r '{}' + && \
    rm -rf /root/.cache && \
    rm -rf /tmp/*

# Run FAVITES
ENTRYPOINT ["/bin/bash", "-c", "run_favites.py"]