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Dockerfile
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FROM ubuntu:20.04 as base
LABEL org.label-schema.name="LDServer"
LABEL org.label-schema.description="LDServer for calculating linkage disequilibrium of genetic variants"
LABEL org.label-schema.vendor="University of Michigan, Center for Statistical Genetics"
LABEL org.label-schema.url="https://github.com/statgen/LDServer"
LABEL org.label-schema.usage="https://github.com/statgen/LDServer#docker"
LABEL org.label-schema.vcs-url="https://github.com/statgen/LDServer"
LABEL org.label-schema.schema-version="1.0"
# Install required packages for LDServer to install.
ENV DEBIAN_FRONTEND="noninteractive"
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential \
curl \
cmake \
python3 \
python3-dev \
python3-distutils \
python3-setuptools \
python3-pip \
python3-wheel \
zlib1g-dev \
liblzma-dev \
redis \
locales \
git \
pkg-config \
sqlite3 \
&& rm -rf /var/lib/apt/lists/* \
&& locale-gen en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
# Set a default # of threads, otherwise OMP decides to use every core it possibly can,
# which can cause some strange runtime issues. These variables can be overridden by using
# a .env file with docker compose, for example.
ENV OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1
# Upgrade pip
RUN pip3 install --upgrade pip
# Install required python packages for building later packages
COPY rest/build.txt /
RUN pip3 install -r build.txt
# Create a group and user to execute as, then drop root
ARG UID
ARG GID
RUN \
if [ -n "$GID" ]; then \
addgroup --gid $GID ldserver; \
else \
addgroup ldserver; \
fi && \
if [ -n "$UID" ]; then \
adduser --gecos "User for running LDServer as non-root" --shell /bin/bash --disabled-password --uid $UID --ingroup ldserver ldserver; \
else \
adduser --gecos "User for running LDServer as non-root" --shell /bin/bash --disabled-password --ingroup ldserver ldserver; \
fi
WORKDIR /home/ldserver
USER ldserver
# Install cpp dependencies
COPY --chown=ldserver:ldserver core/requirements.txt /home/ldserver/core/requirements.txt
COPY --chown=ldserver:ldserver core/*.cmake /home/ldserver/core/
ARG CMAKE_BUILD_PARALLEL_LEVEL
ARG MAKEFLAGS
RUN cget install -f core/requirements.txt
# Install required python packages
ENV PATH="/home/ldserver/.local/bin:${PATH}"
COPY --chown=ldserver:ldserver rest/requirements.txt rest/requirements.txt
RUN pip3 install -r rest/requirements.txt
# Next stage: compiled server/binaries
FROM base as compile
# Copy required test data
# This must happen before compile unfortunately, as cmake install will try to symlink test files
# into its own test directory
COPY --chown=ldserver:ldserver ./data /home/ldserver/data
# Copy source
COPY --chown=ldserver:ldserver CMakeLists.txt /home/ldserver/CMakeLists.txt
COPY --chown=ldserver:ldserver ./core /home/ldserver/core
RUN mkdir -p rest
# Compile ldserver cpp
ENV CGET_PREFIX="/home/ldserver/cget"
ENV INSTALL_PREFIX="/home/ldserver/cget"
RUN \
mkdir build \
&& cd build \
&& cmake .. \
-DCMAKE_TOOLCHAIN_FILE=${CGET_PREFIX}/cget/cget.cmake \
-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
-DCMAKE_BUILD_TYPE=Release \
&& cmake --build . --target install
# Copy python/flask, other scripts
COPY --chown=ldserver:ldserver ./rest /home/ldserver/rest
COPY --chown=ldserver:ldserver ./bin /home/ldserver/bin
# Run test cases
FROM compile as test
COPY --chown=ldserver:ldserver tox.ini /home/ldserver/tox.ini
RUN tox && python3 bin/test_gunicorn.py && rm -f ./rest/ldserver/sql.db
# Frequently changing metadata here to avoid cache misses
ARG BUILD_DATE
ARG GIT_SHA
ARG LDSERVER_VERSION
LABEL org.label-schema.version=$LDSERVER_VERSION \
org.label-schema.vcs-ref=$GIT_SHA \
org.label-schema.build-date=$BUILD_DATE
# Set the default stage to be the base files + compiled binaries + test cases.
FROM test