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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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