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Dockerfile
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FROM ubuntu:20.04 as builder
# Locale
ENV LC_ALL C
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
# ensure any pipes fail correctly, may impact other things
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
# work in an area that will get discarded
WORKDIR /tmp/build
# Prevent interactive options during installs
ENV DEBIAN_FRONTEND=noninteractive
# apt stuff
# hadolint ignore=DL3008
RUN apt-get -yq update \
&& apt-get -yq install --no-install-recommends software-properties-common \
&& add-apt-repository ppa:deadsnakes/ppa \
&& apt-get -yq install --no-install-recommends python3.9 \
&& update-alternatives --install /usr/bin/python python /usr/bin/python3.9 1
# not in final image
# hadolint ignore=DL3008
RUN apt-get -yq update \
&& apt-get -yq install --no-install-recommends \
build-essential \
python3.9-dev \
python3.9-distutils \
python3.9-venv \
time \
tabix \
bcftools \
curl \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-openssl-dev \
libmagic-dev \
&& curl -sSL --retry 10 https://bootstrap.pypa.io/get-pip.py > get-pip.py \
&& python3.9 get-pip.py
# base environment
ENV OPT /opt/wsi-t78
ENV VIRTUAL_ENV=$OPT/venv
RUN python3.9 -m venv $VIRTUAL_ENV
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
COPY annotate/ annotate/
COPY README.md setup.py requirements.txt requirements_dev.txt run_tests.sh ./
RUN pip install --no-cache-dir -r requirements_dev.txt
COPY tests/ tests/
#COPY .coveragerc .
RUN python3.9 ./setup.py develop && ./run_tests.sh
# generate the coverage report (and junit.xml) in for info and later use
RUN mkdir -p /var/www/annotateVCF && mv htmlcov /var/www/annotateVCF/test-coverage
# as we use COPY we can cleanup stuff from the testing layers and actually get a smaller image
RUN comm -13 <(sort requirements.txt) <(sort requirements_dev.txt) | xargs pip uninstall -y
# deploy properly
RUN python3.9 ./setup.py install \
# make sure permissions are correct
&& find $OPT -type d -exec chmod o+rx {} \; \
&& find $OPT -type f -exec chmod o+r {} \;
########################## FINAL IMAGE ##########################
FROM ubuntu:20.04
# Locale
ENV LC_ALL C
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
# Prevent interactive options during installs
ENV DEBIAN_FRONTEND=noninteractive
# apt stuff
# hadolint ignore=DL3008
RUN apt-get -yq update \
&& apt-get -yq install --no-install-recommends software-properties-common libmagic-dev zlib1g curl \
&& add-apt-repository ppa:deadsnakes/ppa \
&& apt-get -yq install --no-install-recommends python3.9 \
time \
tabix \
bcftools \
curl \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-openssl-dev \
libmagic-dev \
# make sure all security patches are applied
&& apt-get -yq update && apt-get install -yq --no-install-recommends unattended-upgrades \
&& unattended-upgrade -d -v \
&& apt-get remove -yq unattended-upgrades \
&& apt-get autoremove -yq \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& update-alternatives --install /usr/bin/python python /usr/bin/python3.9 1
ENV OPT /opt/wsi-t78
ENV VIRTUAL_ENV=$OPT/venv
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
COPY --from=builder $OPT $OPT
# the test coverage html output - we can grab and pass to gitlab-pages
COPY --from=builder /var/www/ /var/www/
RUN annotateVcf --version
RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
USER ubuntu
WORKDIR /home/ubuntu
CMD ["/bin/bash"]