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Optimise Dockerfiles to reduce final image size #864

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21 changes: 14 additions & 7 deletions Dockerfiles/murfey-instrument-server
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@
FROM docker.io/library/python:3.12-slim-bookworm AS base

# Install Vim in base image
RUN apt-get update && \
RUN \
echo "Setting up base image..." && \
apt-get update && \
apt-get upgrade -y && \
apt-get install -y --no-install-recommends \
rsync \
Expand All @@ -17,8 +19,11 @@ RUN apt-get update && \

# Build Murfey in a branch image
FROM base as build
COPY ./ /python-murfey/
RUN apt-get update && \

RUN \
--mount=type=bind,source=.,target=/mnt/python-murfey,U \
echo "Installing build dependencies..." && \
apt-get update && \
apt-get upgrade -y && \
apt-get install -y --no-install-recommends \
build-essential \
Expand All @@ -27,12 +32,14 @@ RUN apt-get update && \
libpq-dev \
&& \
busybox --install && \
echo "Installing Murfey..." && \
cp -r /mnt/python-murfey /tmp/python-murfey && \
python -m venv /venv && \
/venv/bin/python -m pip install --upgrade \
pip \
build \
importlib-metadata && \
/venv/bin/python -m pip install /python-murfey[sxt]
/venv/bin/python -m pip install /tmp/python-murfey[sxt]


# Transfer completed Murfey build to base image
Expand All @@ -44,10 +51,10 @@ ARG groupname
ARG userid

# Copy completed Murfey build across and set user and group permissions
COPY --from=build /venv/ /venv/
RUN groupadd -r -g "${groupid}" "${groupname}" && \
COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/
RUN \
groupadd -r -g "${groupid}" "${groupname}" && \
useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \
chown -R "${userid}":"${groupid}" /venv && \
chmod -R a+x /venv
ENV PATH=/venv/bin:$PATH
USER "${userid}":"${groupid}"
52 changes: 28 additions & 24 deletions Dockerfiles/murfey-server
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Original file line number Diff line number Diff line change
Expand Up @@ -5,48 +5,52 @@
FROM docker.io/library/python:3.12-slim-bookworm AS base

# Install Vim and PostgreSQL dependencies in base image
RUN apt-get update && \
RUN \
echo "Setting up base image..." && \
apt-get update && \
apt-get upgrade -y && \
apt-get install -y --no-install-recommends \
libpq-dev \
vim \
&& \
vim && \
apt-get autoremove && \
rm -rf /var/lib/apt/lists/*


# Build Murfey and IMOD in a branch image
FROM base as build

# Set up build argumentss for this stage
ARG IMOD_INSTALLER=imod_5.1.9_RHEL8-64_CUDA12.0.sh

COPY ./ /python-murfey/
RUN apt-get update && \
RUN \
--mount=type=bind,source=.,target=/mnt/python-murfey,U \
echo "Installing build dependencies..." && \
apt-get update && \
apt-get upgrade -y && \
apt-get install -y --no-install-recommends \
build-essential \
busybox \
curl \
net-tools \
&& \
net-tools && \
busybox --install && \
echo "Installing Murfey..." && \
cp -r /mnt/python-murfey /tmp/python-murfey && \
python -m venv /venv && \
/venv/bin/python -m pip install --upgrade \
pip \
build \
importlib-metadata \
psycopg2-binary \
&& \
/venv/bin/python -m pip install /python-murfey[server] && \
if [ ! -f /python-murfey/installers/${IMOD_INSTALLER} ]; then \
psycopg2-binary && \
/venv/bin/python -m pip install /tmp/python-murfey[server] && \
echo "Installing IMOD..." && \
mkdir /imod && \
if [ -f /mnt/python-murfey/installers/${IMOD_INSTALLER} ]; then \
bash "/mnt/python-murfey/installers/${IMOD_INSTALLER}" -dir /imod -skip -y; \
else \
echo "IMOD installer not found; downloading..."; \
curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD_INSTALLER} > /python-murfey/installers/${IMOD_INSTALLER}; \
fi && \
chmod +x /python-murfey/installers/${IMOD_INSTALLER} && \
mkdir imod && \
/python-murfey/installers/${IMOD_INSTALLER} -dir imod -skip -y

curl -L \
-o "/tmp/${IMOD_INSTALLER}" \
https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD_INSTALLER}; \
bash "/tmp/${IMOD_INSTALLER}" -dir /imod -skip -y; \
fi

# Transfer completed builds to base image
FROM base
Expand All @@ -57,12 +61,12 @@ ARG groupname
ARG userid

# Copy completed Murfey and IMOD builds across and set user and group permissions
COPY --from=build /venv/ /venv/
COPY --from=build /imod/ /imod/
RUN groupadd -r -g "${groupid}" "${groupname}" && \
COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/
COPY --from=build --chown="${userid}":"${groupid}" /imod/ /imod/
RUN \
groupadd -r -g "${groupid}" "${groupname}" && \
useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \
chown -R "${userid}":"${groupid}" /venv && \
chmod -R a+x /venv
chmod -R a+x /venv /imod
ENV PATH=/venv/bin:/imod/IMOD/bin:$PATH
ENV IMOD_DIR=/imod/IMOD
USER "${userid}":"${groupid}"