Oligotyping_Dockerfile_v2.1.sh

FROM ubuntu:xenial

ENV OLIGOTYPING_VERSION 2.1

ENV DEBIAN_FRONTEND noninteractive

RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
RUN apt-get update
RUN apt-get install locales
RUN locale-gen en_US.UTF-8
ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8'

RUN apt-get install -y --no-install-recommends \
        build-essential \
        gsl-bin \
        python \
        python-pip \
        python-dev \
        python-numpy \
        python-scipy \
        python-networkx \
        r-base \
        r-base-dev \
        wget \
        git \
        nano \
        bsdmainutils \
        libblas-dev \
        liblapack-dev \
        libatlas-base-dev \
        libssl-dev \
        gfortran \
        zlib1g-dev \
        libhdf5-serial-dev \
        libhdf5-dev \
        mcl \
        ncbi-blast+ \
        muscle \
        python-tk \
    && mkdir -p /tmp/build \
    && wget https://github.com/bbuchfink/diamond/releases/download/v0.8.38/diamond-linux64.tar.gz -O /tmp/build/diamond-linux64.tar.gz \
    && tar -zxvf /tmp/build/diamond-linux64.tar.gz -C /tmp/build/ \
    && cp /tmp/build/diamond /usr/bin/ \
    && pip install --upgrade pip \
    && pip install setuptools \
    && pip install \
        Matplotlib==2.0.2 \
		BioPython==1.69 \
        cython==0.25.2 \
        pysam==0.11.1 \
        django==1.9.7 \
        requests==2.10.0 \
        six==1.10.0 \
    && pip install --no-deps oligotyping==$OLIGOTYPING_VERSION

RUN echo "export PS1=\"\[\e[0m\e[47m\e[1;30m\] :: oligotyping :: \[\e[0m\e[0m \[\e[1;34m\]\]\w\[\e[m\] \[\e[1;32m\]>>>\[\e[m\] \[\e[0m\]\"" >> /root/.bashrc

RUN Rscript -e "install.packages(c('vegan', 'ggplot2', 'gplots', 'gtools', 'reshape', 'optparse', 'pheatmap', 'RColorBrewer', 'compute.es'), '/usr/local/lib/R/site-library', 'http://ftp.ussg.iu.edu/CRAN/')"
RUN mkdir -p /root/.config/matplotlib
RUN echo 'backend: Agg' > /root/.config/matplotlib/matplotlibrc

RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/*

CMD /bin/bash -l