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FROM debian:stretch
ENV DEBIAN_FRONTEND noninteractive
### RUN set -ex; \
RUN apt-get update -qq; \
apt-get install -y -qq git \
apt-utils \
wget \
python3-pip \
ncbi-blast+ \
libz-dev \
; \
rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
ENV DEBIAN_FRONTEND Teletype
# Install python dependencies
RUN pip3 install -U biopython==1.73 tabulate cgecore==1.4.2;
# Install kma
RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \
cd kma && make; \
mv kma* /bin/
COPY virulencefinder.py /usr/src/virulencefinder.py
# TEST setup
RUN mkdir /database /test
COPY test/database/ /database/
COPY test/test* test/
COPY virulencefinder.py /usr/src/virulencefinder.py
RUN chmod 755 /usr/src/virulencefinder.py; \
chmod 755 test/test.sh
ENV PATH $PATH:/usr/src
# Setup .bashrc file for convenience during debugging
RUN echo "alias ls='ls -h --color=tty'\n"\
"alias ll='ls -lrt'\n"\
"alias l='less'\n"\
"alias du='du -hP --max-depth=1'\n"\
"alias cwd='readlink -f .'\n"\
"PATH=$PATH\n">> ~/.bashrc
WORKDIR /workdir
# Execute program when running the container
ENTRYPOINT ["/usr/src/virulencefinder.py"]
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