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Switch Dockerfiles to python:3.10-slim-bookworm for lighter images #295

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Initial plan
Copilot Dec 3, 2025
852194e
Switch both Dockerfiles from ubuntu:22.04 to python:3.10-slim-bookworm
Copilot Dec 3, 2025
a6193fb
Add documentation comments about base image changes
Copilot Dec 3, 2025
a56eeee
Address code review feedback: consolidate RUN commands and improve do…
Copilot Dec 3, 2025
3bbd825
Improve pyOpenMS copy documentation to clarify wildcard pattern
Copilot Dec 3, 2025
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87 changes: 79 additions & 8 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# This Dockerfile builds OpenMS, the TOPP tools, pyOpenMS and thidparty tools.
# This Dockerfile builds OpenMS, the TOPP tools, pyOpenMS and thirdparty tools.
# It also adds a basic streamlit server that serves a pyOpenMS-based app.
# Uses multi-stage build: Ubuntu for compilation, python:3.10-slim-bookworm for runtime (~150MB lighter)
# hints:
# build image and give it a name (here: streamlitapp) with: docker build --no-cache -t streamlitapp:latest --build-arg GITHUB_TOKEN=<your-github-token> . 2>&1 | tee build.log
# check if image was build: docker image ls
Expand Down Expand Up @@ -117,7 +118,79 @@ ENV OPENMS_DATA_PATH="/openms/share/"
RUN rm -rf openms-build

# Prepare and run streamlit app.
FROM compile-openms AS run-app
# Use a minimal Python base image for the runtime
FROM python:3.10-slim-bookworm AS run-app
ARG PORT=8501
ARG GITHUB_TOKEN
ENV GH_TOKEN=${GITHUB_TOKEN}
ARG GITHUB_USER=OpenMS
ARG GITHUB_REPO=streamlit-template

USER root

# Install only runtime dependencies (not build dependencies)
RUN apt-get -y update && apt-get install -y --no-install-recommends --no-install-suggests \
libgtk2.0-0 \
libsvm3 \
libglpk40 \
libzip4 \
zlib1g \
libxerces-c3.2 \
libbz2-1.0 \
libomp5 \
libhdf5-103-1 \
libboost-date-time1.74.0 \
libboost-iostreams1.74.0 \
libboost-regex1.74.0 \
libboost-math1.74.0 \
libboost-random1.74.0 \
libqt6core6 \
libqt6gui6 \
libqt6widgets6 \
libqt6svg6 \
libqt6opengl6 \
libqt6openglwidgets6 \
libgl1 \
openjdk-17-jre-headless \
curl \
jq \
cron \
gnupg \
wget \
ca-certificates \
&& rm -rf /var/lib/apt/lists/*
RUN update-ca-certificates

# Install Github CLI (needed for downloading artifacts)
RUN mkdir -p -m 755 /etc/apt/keyrings \
&& wget -qO- https://cli.github.com/packages/githubcli-archive-keyring.gpg | tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
&& chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& apt-get update \
&& apt-get install gh -y \
&& rm -rf /var/lib/apt/lists/*

# Copy OpenMS binaries and libraries from the build stage
COPY --from=compile-openms /openms /openms
COPY --from=compile-openms /thirdparty /thirdparty

# Set environment variables for OpenMS
ENV PATH="/openms/bin/:/thirdparty/LuciPHOr2:/thirdparty/MSGFPlus:/thirdparty/Sirius:/thirdparty/ThermoRawFileParser:/thirdparty/Comet:/thirdparty/Fido:/thirdparty/MaRaCluster:/thirdparty/MyriMatch:/thirdparty/OMSSA:/thirdparty/Percolator:/thirdparty/SpectraST:/thirdparty/XTandem:/thirdparty/crux:${PATH}"
ENV LD_LIBRARY_PATH="/openms/lib/:${LD_LIBRARY_PATH}"
ENV OPENMS_DATA_PATH="/openms/share/"

# Install Python dependencies and copy pyOpenMS from build stage
COPY requirements.txt ./requirements.txt
RUN python -m pip install --upgrade pip && \
grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && \
mv requirements_cleaned.txt requirements.txt && \
python -m pip install -r requirements.txt

# Copy pyOpenMS from build stage (built with mamba in compile-openms stage)
# Source path is from mamba environment, target is system site-packages
# The wildcard matches both pyopenms/ package dir and pyopenms-*.dist-info/ metadata
COPY --from=compile-openms /root/miniforge3/envs/streamlit-env/lib/python3.10/site-packages/pyopenms* /usr/local/lib/python3.10/site-packages/

# Create workdir and copy over all streamlit related files/folders.

# note: specifying folder with slash as suffix and repeating the folder name seems important to preserve directory structure
Expand All @@ -139,18 +212,16 @@ COPY .streamlit/config.toml /app/.streamlit/config.toml
COPY clean-up-workspaces.py /app/clean-up-workspaces.py

# add cron job to the crontab
RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
RUN echo "0 3 * * * /usr/local/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -

# create entrypoint script to start cron service and launch streamlit app
RUN echo "#!/bin/bash" > /app/entrypoint.sh && \
echo "source /root/miniforge3/bin/activate streamlit-env" >> /app/entrypoint.sh && \
echo "service cron start" >> /app/entrypoint.sh && \
echo "streamlit run app.py" >> /app/entrypoint.sh
# make the script executable
RUN chmod +x /app/entrypoint.sh
echo "streamlit run app.py" >> /app/entrypoint.sh && \
chmod +x /app/entrypoint.sh

# Patch Analytics
RUN mamba run -n streamlit-env python hooks/hook-analytics.py
RUN python hooks/hook-analytics.py

# Set Online Deployment
RUN jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json
Expand Down
64 changes: 25 additions & 39 deletions Dockerfile_simple
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Original file line number Diff line number Diff line change
@@ -1,13 +1,14 @@
# This Dockerfile creates a container with pyOpenMS
# It also adds a basic streamlit server that serves a pyOpenMS-based app.
# Uses python:3.10-slim-bookworm as base image for smaller image size (~150MB vs ~700MB for ubuntu:22.04)
# hints:
# build image with: docker build -f Dockerfile_simple --no-cache -t streamlitapp:latest --build-arg GITHUB_TOKEN=<your-github-token> . 2>&1 | tee build.log
# check if image was build: docker image ls
# run container: docker run -p 8501:8501 streamlitapp:latest
# debug container after build (comment out ENTRYPOINT) and run container with interactive /bin/bash shell
# prune unused images/etc. to free disc space (e.g. might be needed on gitpod). Use with care.: docker system prune --all --force

FROM ubuntu:22.04 AS stage1
FROM python:3.10-slim-bookworm AS stage1
ARG OPENMS_REPO=https://github.com/OpenMS/OpenMS.git
ARG OPENMS_BRANCH=develop
ARG PORT=8501
Expand All @@ -23,38 +24,28 @@ ARG GITHUB_REPO=streamlit-template
# Step 1: set up a sane build system
USER root

RUN apt-get -y update
# note: streamlit in docker needs libgtk2.0-dev (see https://yugdamor.medium.com/importerror-libgthread-2-0-so-0-cannot-open-shared-object-file-no-such-file-or-directory-895b94a7827b)
RUN apt-get install -y --no-install-recommends --no-install-suggests wget ca-certificates libgtk2.0-dev curl jq cron
RUN apt-get -y update && apt-get install -y --no-install-recommends --no-install-suggests \
wget \
ca-certificates \
libgtk2.0-0 \
curl \
jq \
cron \
gnupg \
&& rm -rf /var/lib/apt/lists/*
RUN update-ca-certificates

# Install Github CLI
RUN (type -p wget >/dev/null || (apt-get update && apt-get install wget -y)) \
&& mkdir -p -m 755 /etc/apt/keyrings \
&& wget -qO- https://cli.github.com/packages/githubcli-archive-keyring.gpg | tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
&& chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& apt-get update \
&& apt-get install gh -y

# Download and install miniforge.
ENV PATH="/root/miniforge3/bin:${PATH}"
RUN wget -q \
https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
&& bash Miniforge3-Linux-x86_64.sh -b \
&& rm -f Miniforge3-Linux-x86_64.sh
RUN mamba --version

# Setup mamba environment.
RUN mamba create -n streamlit-env python=3.10
RUN echo "mamba activate streamlit-env" >> ~/.bashrc
SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]

#################################### install streamlit
# install packages
RUN mkdir -p -m 755 /etc/apt/keyrings \
&& wget -qO- https://cli.github.com/packages/githubcli-archive-keyring.gpg | tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
&& chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& apt-get update \
&& apt-get install gh -y \
&& rm -rf /var/lib/apt/lists/*

# Install packages
COPY requirements.txt requirements.txt
RUN mamba install pip
RUN python -m pip install --upgrade pip
RUN python -m pip install -r requirements.txt

Expand All @@ -81,18 +72,16 @@ COPY .streamlit/config.toml /app/.streamlit/config.toml
COPY clean-up-workspaces.py /app/clean-up-workspaces.py

# add cron job to the crontab
RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
RUN echo "0 3 * * * /usr/local/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -

# create entrypoint script to start cron service and launch streamlit app
RUN echo "#!/bin/bash" > /app/entrypoint.sh
RUN echo "source /root/miniforge3/bin/activate streamlit-env" >> /app/entrypoint.sh && \
RUN echo "#!/bin/bash" > /app/entrypoint.sh && \
echo "service cron start" >> /app/entrypoint.sh && \
echo "streamlit run app.py" >> /app/entrypoint.sh
# make the script executable
RUN chmod +x /app/entrypoint.sh
echo "streamlit run app.py" >> /app/entrypoint.sh && \
chmod +x /app/entrypoint.sh

# Patch Analytics
RUN mamba run -n streamlit-env python hooks/hook-analytics.py
RUN python hooks/hook-analytics.py

# Set Online Deployment
RUN jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json
Expand All @@ -105,8 +94,5 @@ RUN if [ -n "$GH_TOKEN" ]; then \
echo "GH_TOKEN is not set, skipping the release asset download."; \
fi

# make sure that mamba environment is used
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]

EXPOSE $PORT
ENTRYPOINT ["/app/entrypoint.sh"]
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