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‎Dockerfile‎

Lines changed: 75 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,15 @@
1-
# This Dockerfile creates a container with pyOpenMS
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# This Dockerfile builds OpenMS, the TOPP tools, pyOpenMS and thidparty tools.
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# It also adds a basic streamlit server that serves a pyOpenMS-based app.
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# hints:
4-
# 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
4+
# 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
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# check if image was build: docker image ls
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# run container: docker run -p 8501:8501 streamlitapp:latest
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# run container: docker run -p 8501:8501 streamlitappsimple:latest
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# debug container after build (comment out ENTRYPOINT) and run container with interactive /bin/bash shell
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# prune unused images/etc. to free disc space (e.g. might be needed on gitpod). Use with care.: docker system prune --all --force
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10-
FROM ubuntu:22.04 AS stage1
10+
FROM ubuntu:22.04 AS setup-build-system
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ARG OPENMS_REPO=https://github.com/OpenMS/OpenMS.git
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ARG OPENMS_BRANCH=develop
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ARG OPENMS_BRANCH=release/3.2.0
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ARG PORT=8501
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# GitHub token to download latest OpenMS executable for Windows from Github action artifact.
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ARG GITHUB_TOKEN
@@ -19,14 +19,19 @@ ARG GITHUB_USER=OpenMS
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# Streamlit app Gihub repository name (to download artifact from).
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ARG GITHUB_REPO=streamlit-template
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# Step 1: set up a sane build system
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USER root
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# Install required Ubuntu packages.
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RUN apt-get -y update
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# 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)
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RUN apt-get install -y --no-install-recommends --no-install-suggests wget ca-certificates libgtk2.0-dev curl jq cron
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RUN apt-get install -y --no-install-recommends --no-install-suggests g++ autoconf automake patch libtool make git gpg wget ca-certificates curl jq libgtk2.0-dev openjdk-8-jdk cron
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RUN update-ca-certificates
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RUN apt-get install -y --no-install-recommends --no-install-suggests libsvm-dev libeigen3-dev coinor-libcbc-dev libglpk-dev libzip-dev zlib1g-dev libxerces-c-dev libbz2-dev libomp-dev libhdf5-dev
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RUN apt-get install -y --no-install-recommends --no-install-suggests libboost-date-time1.74-dev \
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libboost-iostreams1.74-dev \
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libboost-regex1.74-dev \
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libboost-math1.74-dev \
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libboost-random1.74-dev
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RUN apt-get install -y --no-install-recommends --no-install-suggests qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
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# Install Github CLI
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RUN (type -p wget >/dev/null || (apt-get update && apt-get install wget -y)) \
@@ -52,16 +57,66 @@ RUN echo "mamba activate streamlit-env" >> ~/.bashrc
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SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
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SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
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#################################### install streamlit
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# install packages
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COPY requirements.txt requirements.txt
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RUN mamba install pip
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RUN python -m pip install --upgrade pip
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RUN python -m pip install -r requirements.txt
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# Install up-to-date cmake via mamba and packages for pyOpenMS build.
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RUN mamba install cmake
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RUN pip install --upgrade pip && python -m pip install -U setuptools nose Cython autowrap pandas numpy pytest
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# Clone OpenMS branch and the associcated contrib+thirdparties+pyOpenMS-doc submodules.
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RUN git clone --recursive --depth=1 -b ${OPENMS_BRANCH} --single-branch ${OPENMS_REPO} && cd /OpenMS
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# Pull Linux compatible third-party dependencies and store them in directory thirdparty.
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WORKDIR /OpenMS
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RUN mkdir /thirdparty && \
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git submodule update --init THIRDPARTY && \
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cp -r THIRDPARTY/All/* /thirdparty && \
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cp -r THIRDPARTY/Linux/64bit/* /thirdparty && \
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chmod -R +x /thirdparty
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ENV PATH="/thirdparty/LuciPHOr2:/thirdparty/MSGFPlus:/thirdparty/Sirius:/thirdparty/ThermoRawFileParser:/thirdparty/Comet:/thirdparty/Fido:/thirdparty/MaRaCluster:/thirdparty/MyriMatch:/thirdparty/OMSSA:/thirdparty/Percolator:/thirdparty/SpectraST:/thirdparty/XTandem:/thirdparty/crux:${PATH}"
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# Build OpenMS and pyOpenMS.
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FROM setup-build-system AS compile-openms
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WORKDIR /
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# Set up build directory.
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RUN mkdir /openms-build
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WORKDIR /openms-build
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# Configure.
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RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On"
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# Build TOPP tools and clean up.
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RUN make -j4 TOPP
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RUN rm -rf src doc CMakeFiles
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# Build pyOpenMS wheels and install via pip.
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RUN make -j4 pyopenms
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WORKDIR /openms-build/pyOpenMS
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RUN pip install dist/*.whl
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WORKDIR /
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RUN mkdir openms
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# Copy TOPP tools bin directory, add to PATH.
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RUN cp -r openms-build/bin /openms/bin
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ENV PATH="/openms/bin/:${PATH}"
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# Copy TOPP tools bin directory, add to PATH.
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RUN cp -r openms-build/lib /openms/lib
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ENV LD_LIBRARY_PATH="/openms/lib/:${LD_LIBRARY_PATH}"
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# Copy share folder, add to PATH, remove source directory.
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RUN cp -r OpenMS/share/OpenMS /openms/share
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RUN rm -rf OpenMS
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ENV OPENMS_DATA_PATH="/openms/share/"
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# Remove build directory.
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RUN rm -rf openms-build
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# Prepare and run streamlit app.
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FROM compile-openms AS run-app
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# Create workdir and copy over all streamlit related files/folders.
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# create workdir and copy over all streamlit related files/folders
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WORKDIR /app
65120
# note: specifying folder with slash as suffix and repeating the folder name seems important to preserve directory structure
66121
WORKDIR /app
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COPY assets/ /app/assets
@@ -77,15 +132,14 @@ COPY default-parameters.json /app/default-parameters.json
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# For streamlit configuration
79134
COPY .streamlit/config.toml /app/.streamlit/config.toml
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COPY clean-up-workspaces.py /app/clean-up-workspaces.py
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# add cron job to the crontab
84138
RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
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# create entrypoint script to start cron service and launch streamlit app
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RUN echo "#!/bin/bash" > /app/entrypoint.sh
88-
RUN echo "source /root/miniforge3/bin/activate streamlit-env" >> /app/entrypoint.sh && \
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RUN echo "#!/bin/bash" > /app/entrypoint.sh && \
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echo "source /root/miniforge3/bin/activate streamlit-env" >> /app/entrypoint.sh && \
89143
echo "service cron start" >> /app/entrypoint.sh && \
90144
echo "streamlit run app.py" >> /app/entrypoint.sh
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# make the script executable
@@ -105,8 +159,6 @@ RUN if [ -n "$GH_TOKEN" ]; then \
105159
echo "GH_TOKEN is not set, skipping the release asset download."; \
106160
fi
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# make sure that mamba environment is used
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SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
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162+
# Run app as container entrypoint.
111163
EXPOSE $PORT
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ENTRYPOINT ["/app/entrypoint.sh"]

‎Dockerfile_simple‎

Lines changed: 112 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,112 @@
1+
# This Dockerfile creates a container with pyOpenMS
2+
# It also adds a basic streamlit server that serves a pyOpenMS-based app.
3+
# hints:
4+
# 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
5+
# check if image was build: docker image ls
6+
# run container: docker run -p 8501:8501 streamlitapp:latest
7+
# debug container after build (comment out ENTRYPOINT) and run container with interactive /bin/bash shell
8+
# prune unused images/etc. to free disc space (e.g. might be needed on gitpod). Use with care.: docker system prune --all --force
9+
10+
FROM ubuntu:22.04 AS stage1
11+
ARG OPENMS_REPO=https://github.com/OpenMS/OpenMS.git
12+
ARG OPENMS_BRANCH=develop
13+
ARG PORT=8501
14+
# GitHub token to download latest OpenMS executable for Windows from Github action artifact.
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ARG GITHUB_TOKEN
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ENV GH_TOKEN=${GITHUB_TOKEN}
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# Streamlit app Gihub user name (to download artifact from).
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ARG GITHUB_USER=OpenMS
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# Streamlit app Gihub repository name (to download artifact from).
20+
ARG GITHUB_REPO=streamlit-template
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22+
23+
# Step 1: set up a sane build system
24+
USER root
25+
26+
RUN apt-get -y update
27+
# note: streamlit in docker needs libgtk2.0-dev (see https://yugdamor.medium.com/importerror-libgthread-2-0-so-0-cannot-open-shared-object-file-no-such-file-or-directory-895b94a7827b)
28+
RUN apt-get install -y --no-install-recommends --no-install-suggests wget ca-certificates libgtk2.0-dev curl jq cron
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RUN update-ca-certificates
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31+
# Install Github CLI
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RUN (type -p wget >/dev/null || (apt-get update && apt-get install wget -y)) \
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&& mkdir -p -m 755 /etc/apt/keyrings \
34+
&& wget -qO- https://cli.github.com/packages/githubcli-archive-keyring.gpg | tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
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&& chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
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&& echo "deb [arch=$(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 \
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&& apt-get update \
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&& apt-get install gh -y
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40+
# Download and install miniforge.
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ENV PATH="/root/miniforge3/bin:${PATH}"
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RUN wget -q \
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https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
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&& bash Miniforge3-Linux-x86_64.sh -b \
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&& rm -f Miniforge3-Linux-x86_64.sh
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RUN mamba --version
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# Setup mamba environment.
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COPY environment.yml ./environment.yml
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RUN mamba env create -f environment.yml
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RUN echo "mamba activate streamlit-env" >> ~/.bashrc
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SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
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SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
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#################################### install streamlit
56+
# install packages
57+
COPY requirements.txt requirements.txt
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RUN mamba install pip
59+
RUN python -m pip install --upgrade pip
60+
RUN python -m pip install -r requirements.txt
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62+
63+
# create workdir and copy over all streamlit related files/folders
64+
WORKDIR /app
65+
# note: specifying folder with slash as suffix and repeating the folder name seems important to preserve directory structure
66+
WORKDIR /app
67+
COPY assets/ /app/assets
68+
COPY content/ /app/content
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COPY docs/ /app/docs
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COPY example-data/ /app/example-data
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COPY gdpr_consent/ /app/gdpr_consent
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COPY hooks/ /app/hooks
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COPY src/ /app/src
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COPY app.py /app/app.py
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COPY settings.json /app/settings.json
76+
COPY default-parameters.json /app/default-parameters.json
77+
78+
# For streamlit configuration
79+
COPY .streamlit/config.toml /app/.streamlit/config.toml
80+
81+
COPY clean-up-workspaces.py /app/clean-up-workspaces.py
82+
83+
# add cron job to the crontab
84+
RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
85+
86+
# create entrypoint script to start cron service and launch streamlit app
87+
RUN echo "#!/bin/bash" > /app/entrypoint.sh
88+
RUN echo "source /root/miniforge3/bin/activate streamlit-env" >> /app/entrypoint.sh && \
89+
echo "service cron start" >> /app/entrypoint.sh && \
90+
echo "streamlit run app.py" >> /app/entrypoint.sh
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# make the script executable
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RUN chmod +x /app/entrypoint.sh
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# Patch Analytics
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RUN mamba run -n streamlit-env python hooks/hook-analytics.py
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# Set Online Deployment
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RUN jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json
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# Download latest OpenMS App executable for Windows from Github actions workflow.
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RUN if [ -n "$GH_TOKEN" ]; then \
102+
echo "GH_TOKEN is set, proceeding to download the release asset..."; \
103+
gh run download -R ${GITHUB_USER}/${GITHUB_REPO} $(gh run list -R ${GITHUB_USER}/${GITHUB_REPO} -b main -e push -s completed -w "Build executable for Windows" --json databaseId -q '.[0].databaseId') -n OpenMS-App --dir /app; \
104+
else \
105+
echo "GH_TOKEN is not set, skipping the release asset download."; \
106+
fi
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108+
# make sure that mamba environment is used
109+
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
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111+
EXPOSE $PORT
112+
ENTRYPOINT ["/app/entrypoint.sh"]

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