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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
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