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FROM ubuntu:18.04
MAINTAINER Shaun Jackman <sjackman@gmail.com>
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
bsdmainutils libgomp1 make openmpi-bin ssh sudo \
&& useradd -m -s /bin/bash abyss \
&& echo 'abyss ALL=(ALL) NOPASSWD:ALL' >>/etc/sudoers
ADD . /tmp/abyss
RUN apt-get install -y --no-install-recommends \
automake g++ libboost-dev libopenmpi-dev libsparsehash-dev \
&& cd /tmp/abyss \
&& ./autogen.sh \
&& mkdir build && cd build \
&& ../configure --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi \
&& make install-strip \
&& rm -rf /tmp/abyss \
&& apt-get autoremove -y binutils \
automake g++ libboost-dev libopenmpi-dev libsparsehash-dev
USER abyss
WORKDIR /home/abyss
ENV SHELL=/bin/bash USER=abyss
ENTRYPOINT ["abyss-pe"]
CMD ["help"]
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