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.k8s_ci.Dockerfile
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.k8s_ci.Dockerfile
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# Stage 1:
# - base: ubuntu (default) OR prebuilt image0
# - install build tools
# - clone playbook
# Stage 2: build galaxy client and server in parallel
# Stage 2.1:
# - run playbook with server build steps only
# - remove build artifacts + files not needed in container
# Stage 2.2:
# - run playbook with client build steps only
# - remove build artifacts + files not needed in container
# Stage 3:
# - create galaxy user + group + directory
# - copy galaxy files from stage 2.1 and 2.2
# - finalize container (set path, user...)
# Init ARGs
ARG ROOT_DIR=/galaxy
ARG SERVER_DIR=$ROOT_DIR/server
# For much faster build time override this with image0 (Dockerfile.0 build):
# docker build --build-arg BASE=<image0 name>...
ARG STAGE1_BASE=python:3.7-slim
ARG FINAL_STAGE_BASE=$STAGE1_BASE
# NOTE: the value of GALAXY_USER must be also hardcoded in COPY in final stage
ARG GALAXY_USER=galaxy
ARG GALAXY_PLAYBOOK_REPO=https://github.com/galaxyproject/galaxy-docker-k8s
#======================================================
# Stage 1 - Setup common requirements for build
#======================================================
FROM $STAGE1_BASE AS stage1
ARG DEBIAN_FRONTEND=noninteractive
ARG SERVER_DIR
ARG GALAXY_PLAYBOOK_REPO
# Init Env
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
# Install build dependencies + ansible
RUN set -xe; \
echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
&& apt-get -qq update && apt-get install -y --no-install-recommends \
locales locales-all \
git \
make \
libc-dev \
bzip2 \
gcc \
&& pip install --no-cache virtualenv 'ansible<2.10' \
&& apt-get autoremove -y && apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/*
# Remove context from previous build; copy current context; run playbook
WORKDIR /tmp/ansible
RUN rm -rf *
ENV LC_ALL en_US.UTF-8
RUN git clone --depth 1 $GALAXY_PLAYBOOK_REPO galaxy-docker
WORKDIR /tmp/ansible/galaxy-docker
RUN ansible-galaxy install -r requirements.yml -p roles --force-with-deps
# Add Galaxy source code
COPY . $SERVER_DIR/
#======================================================
# Stage 2.1 - Build galaxy server
#======================================================
FROM stage1 AS server_build
ARG SERVER_DIR
RUN ansible-playbook -i localhost, playbook.yml -v -e galaxy_build_client=False -e galaxy_virtualenv_command=virtualenv
RUN cat /galaxy/server/lib/galaxy/dependencies/conditional-requirements.txt | grep psycopg2-binary | xargs /galaxy/server/.venv/bin/pip install
# Remove build artifacts + files not needed in container
WORKDIR $SERVER_DIR
# Save commit hash of HEAD before zapping git folder
RUN git rev-parse HEAD > GITREVISION
RUN rm -rf \
.ci \
.git \
.venv/include/node \
.venv/src/node* \
doc \
test \
test-data
# Clean up *all* node_modules, including plugins. Everything is already built+staged.
RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
#======================================================
# Stage 2.2 - Build galaxy client
#======================================================
FROM stage1 AS client_build
ARG SERVER_DIR
RUN ansible-playbook -i localhost, playbook.yml -v --tags "galaxy_build_client" -e galaxy_virtualenv_command=virtualenv
WORKDIR $SERVER_DIR
RUN rm -rf \
.ci \
.git \
.venv/include/node \
.venv/src/node* \
doc \
test \
test-data
# Clean up *all* node_modules, including plugins. Everything is already built+staged.
RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
#======================================================
# Stage 3 - Build final image based on previous stages
#======================================================
FROM $FINAL_STAGE_BASE
ARG DEBIAN_FRONTEND=noninteractive
ARG ROOT_DIR
ARG SERVER_DIR
ARG GALAXY_USER
# Init Env
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
# Install procps (contains kill, ps etc.), less, curl, vim-tiny and nano-tiny
# for convenience and debugging purposes. Nano and vim commands are aliased
# to their tiny variants using the debian alternatives system.
# Bzip2 and virtualenv are installed for backwards compatibility with older
# versions of this image which was based on Ubuntu and contained these
# utilities.
RUN set -xe; \
echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
&& apt-get -qq update && apt-get install -y --no-install-recommends \
locales \
vim-tiny \
nano-tiny \
curl \
procps \
less \
bzip2 \
&& update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 0 \
&& update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 0 \
&& echo "set nocompatible" >> /usr/share/vim/vimrc.tiny \
&& echo "$LANG UTF-8" > /etc/locale.gen \
&& locale-gen $LANG && update-locale LANG=$LANG \
&& apt-get autoremove -y && apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/*
# Create Galaxy user, group, directory; chown
RUN set -xe; \
adduser --system --group $GALAXY_USER \
&& mkdir -p $SERVER_DIR \
&& chown $GALAXY_USER:$GALAXY_USER $ROOT_DIR -R
WORKDIR $ROOT_DIR
# Copy galaxy files to final image
# The chown value MUST be hardcoded (see #35018 at github.com/moby/moby)
COPY --chown=galaxy:galaxy --from=server_build $ROOT_DIR .
COPY --chown=galaxy:galaxy --from=client_build $SERVER_DIR/static ./server/static
WORKDIR $SERVER_DIR
EXPOSE 8080
USER $GALAXY_USER
ENV PATH="$SERVER_DIR/.venv/bin:${PATH}"
ENV GALAXY_CONFIG_CONDA_AUTO_INIT=False
# [optional] to run:
CMD uwsgi --yaml config/galaxy.yml