Dockerfile.backend

FROM ubuntu:22.04

ENV DEBIAN_FRONTEND noninteractive

RUN apt-get -qy update && \
    apt-get -qqy install python3.10-dev python3.10-distutils binutils build-essential git python3-scipy openmpi-bin openmpi-doc libopenmpi-dev r-cran-devtools

ENV OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

ADD https://bootstrap.pypa.io/get-pip.py /tmp/get-pip.py

RUN python3.10 /tmp/get-pip.py
RUN /usr/local/bin/pip install biopython mpi4py rpy2 psycopg2-binary

RUN R -e "install.packages('tidyquant',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('matrixStats',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('ape',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('phytools',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "devtools::install_github('phoscheit/LambdaSkyline')"

ADD http://www.microbesonline.org/fasttree/FastTree.c /root/FastTree.c
RUN gcc -DUSE_DOUBLE -O3 -finline-functions -funroll-loops -Wall -o /usr/local/bin/fasttree2 /root/FastTree.c -lm && \
    chmod u+x /usr/local/bin/fasttree2

RUN git clone --depth=1 https://github.com/lh3/minimap2.git /root/minimap2 && \
    make -C /root/minimap2 && \
    cp /root/minimap2/minimap2 /usr/local/bin

RUN git clone --depth=1 https://github.com/neherlab/treetime.git /root/treetime && \
    /usr/local/bin/pip install /root/treetime

RUN git clone --depth=1 https://github.com/somme89/rapidNJ.git /root/rapidnj && \
    make -C /root/rapidnj && \
    cp /root/rapidnj/bin/rapidnj /usr/local/bin