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# This container will install Circlator from master
#
FROM debian:testing
ENV BUILD_DIR=/opt/circlator
# Install the dependancies
RUN apt-get update -qq && apt-get install -y python python3-pip git wget unzip zlib1g-dev libncurses5-dev
RUN apt-get install --yes libbz2-dev liblzma-dev
RUN mkdir -p ${BUILD_DIR}
COPY . ${BUILD_DIR}
RUN cd ${BUILD_DIR} && ./install_dependencies.sh
ENV PATH ${BUILD_DIR}/build/bwa-0.7.12:${BUILD_DIR}/build/canu-1.4/Linux-amd64/bin/:${BUILD_DIR}/build/prodigal-2.6.2:${BUILD_DIR}/build/samtools-1.3:${BUILD_DIR}/build/MUMmer3.23:${BUILD_DIR}/build/SPAdes-3.7.1-Linux/bin:$PATH
RUN export PATH
RUN cd ${BUILD_DIR} && python3 setup.py install
RUN circlator progcheck
CMD echo "Usage: docker run -v \`pwd\`:/var/data -it <IMAGE_NAME> bash" && \
echo "" && \
echo "This will place you in a shell with your current working directory accessible as /var/data." && \
echo "You can then run commands like:" && \
echo " circlator all /var/data/assembly.fasta /var/data/reads /var/data/<output_subdirectory>" && \
echo "For help, please go to https://github.com/sanger-pathogens/circlator/wiki, or type" && \
echo " circlator --help"
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