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Dockerfile
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FROM ubuntu
MAINTAINER Paul Pham <[email protected]>
ENV build=/circlator/build\
spades=SPAdes-3.7.1-Linux\
samtools=samtools-1.3\
mummer=MUMmer3.23\
prodigal=prodigal-2.6.2\
bwa=bwa-0.7.12\
bin=/usr/local/bin\
root=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ENV PATH=${root}:${build}/${spades}/bin:${build}/${mummer}
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y make g++ zlib1g-dev ncurses-dev git python3 python3-pip wget csh \
&& ln -s /usr/bin/python3 /usr/bin/python \
&& git clone https://github.com/sanger-pathogens/circlator \
&& cd /circlator \
&& bash install_dependencies.sh \
&& export PATH="${PATH}" \
&& cd ${build} \
&& cp ${prodigal}/prodigal ${bin} \
&& cp ${bwa}/bwa ${bin} \
&& cd ${samtools}; make install; cd .. \
&& rm -rf *.gz *.bz2 \
&& pip3 install --upgrade --no-cache-dir pip \
&& pip3 install --no-cache-dir circlator \
&& circlator progcheck \
&& apt-get install --purge make g++ zlib1g-dev ncurses-dev git wget csh \
&& apt-get autoclean
WORKDIR /data
ENTRYPOINT ["circlator"]