Mercurial > repos > dcouvin > resfinder4
view resfinder/dockerfile @ 0:55051a9bc58d draft default tip
Uploaded
author | dcouvin |
---|---|
date | Mon, 10 Jan 2022 20:06:07 +0000 |
parents | |
children |
line wrap: on
line source
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 gitpython python-dateutil; # RESFINDER setup COPY run_resfinder.py /usr/src/run_resfinder.py ADD cge /usr/src/cge ADD tests /usr/src/tests # Install kma RUN cd /usr/src/cge; \ git clone --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \ cd kma && make; \ mv kma* /bin/ RUN chmod 755 /usr/src/run_resfinder.py RUN chmod 755 /usr/src/tests/functional_tests.py 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 # Change working directory WORKDIR "/usr/src/" # Execute program when running the container ENTRYPOINT ["python3", "/usr/src/run_resfinder.py"]