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# Multi-container Dockerfile for build and run containers for vg
FROM ubuntu:18.04 AS base
MAINTAINER vgteam
RUN echo base > /stage.txt
WORKDIR /vg
# Prevent dpkg from trying to ask any questions, ever
ENV DEBIAN_FRONTEND noninteractive
ENV DEBCONF_NONINTERACTIVE_SEEN true
FROM base AS build
ARG THREADS=8
RUN echo build > /stage.txt
# Copy vg build tree into place
COPY . /vg
# Install the base packages needed to let vg install packages.
# Make sure this runs after vg sources are imported so vg will always have an
# up to date package index to get its dependencies.
# We don't need to clean the package index since we don't ship this image and
# don't care about its size.
# We don't want to install too much stuff here, because we want to test vg's
# make get-deps to make sure it isn't missing something
RUN apt-get -qq -y update && \
apt-get -qq -y upgrade && \
apt-get -qq -y install --no-upgrade \
make \
sudo \
git
# If we're trying to build from a non-recursively-cloned repo, go get the
# submodules.
RUN bash -c "[[ -e deps/sdsl-lite/CMakeLists.txt ]] || git submodule update --init --recursive"
# To increase portability of the docker image, set the target CPU architecture to
# Nehalem (2008) rather than auto-detecting the build machine's CPU.
# This has no AVX1, AVX2, or PCLMUL, but it does have SSE4.2.
# UCSC has a Nehalem machine that we want to support.
RUN sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt
# Do the build. Trim down the resulting binary but make sure to include enough debug info for profiling.
RUN make get-deps && . ./source_me.sh && env && make include/vg_git_version.hpp && CXXFLAGS=" -march=nehalem " make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) && make static && strip -d bin/vg
ENV PATH /vg/bin:$PATH
############################################################################################
FROM build AS test
ARG THREADS=8
RUN echo test > /stage.txt
# The tests also need some other extra packages.
# TODO: Which of these can we remove?
# No clean necessary since we aren't shipping this
RUN apt-get -qq -y update && \
apt-get -qq -y upgrade && \
apt-get -qq -y install --no-upgrade \
bwa \
pigz \
dstat \
pv \
jq \
samtools \
tabix \
parallel \
bsdmainutils \
rs \
fontconfig-config
# Fail if any non-portable instructions were used
RUN /bin/bash -e -c 'if objdump -d /vg/bin/vg | grep vperm2i128 ; then exit 1 ; else exit 0 ; fi'
# Run tests in the middle so the final container that gets tagged is the run container.
RUN export OMP_NUM_THREADS=$((THREADS < $(nproc) ? THREADS : $(nproc))) make test
############################################################################################
FROM base AS run
RUN echo run > /stage.txt
COPY --from=build /vg/bin/vg /vg/bin/
COPY --from=build /vg/scripts/* /vg/scripts/
# Make sure we have the flame graph scripts so we can do self-profiling
COPY deps/FlameGraph /vg/deps/FlameGraph
# Install packages which toil-vg needs to be available inside the image, for
# pipes and profiling, and good usability on Kubernetes.
# TODO: which of these can be removed?
# Make sure to clean so we don't ship old apt package indexes in our Docker.
RUN ls -lah /vg && \
apt-get -qq -y update && \
apt-get -qq -y upgrade && \
apt-get -qq -y install --no-upgrade \
curl \
wget \
pigz \
dstat \
pv \
jq \
samtools \
tabix \
parallel \
fontconfig-config \
awscli \
binutils \
libssl1.0.0 \
libpython2.7 \
libperl-dev \
libelf1 \
libdw1 \
libslang2 \
libnuma1 \
numactl \
bc \
linux-tools-common \
linux-tools-generic \
perl \
&& apt-get -qq -y clean
ENV PATH /vg/bin:$PATH
|
