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Dockerfile_simple
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# This Dockerfile creates a container with pyOpenMS
# It also adds a basic streamlit server that serves a pyOpenMS-based app.
# 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
ARG OPENMS_REPO=https://github.com/OpenMS/OpenMS.git
ARG OPENMS_BRANCH=release/3.2.0
ARG PORT=8501
# GitHub token to download latest OpenMS executable for Windows from Github action artifact.
ARG GITHUB_TOKEN
# Streamlit app Gihub user name (to download artifact from).
ARG GITHUB_USER=OpenMS
# Streamlit app Gihub repository name (to download artifact from).
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 update-ca-certificates
# 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
# Activate and configure the mamba environment
RUN mamba update -n base -c conda-forge mamba && mamba info && mamba create -n streamlit-env python=3.10
# note: activation of mamba needs to go to bashrc because every RUN command spawns new bash
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
RUN echo "source activate streamlit-env" > ~/.bashrc
#################################### install streamlit
# 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
# create workdir and copy over all streamlit related files/folders
WORKDIR /app
# note: specifying folder with slash as suffix and repeating the folder name seems important to preserve directory structure
WORKDIR /app
COPY assets/ /app/assets
COPY content/ /app/content
COPY docs/ /app/docs
COPY example-data/ /app/example-data
COPY gdpr_consent/ /app/gdpr_consent
COPY hooks/ /app/hooks
COPY src/ /app/src
COPY app.py /app/app.py
COPY settings.json /app/settings.json
COPY default-parameters.json /app/default-parameters.json
# For streamlit configuration
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 -
# create entrypoint script to start cron service and launch streamlit app
RUN echo "#!/bin/bash" > /app/entrypoint.sh
RUN echo "service cron start" >> /app/entrypoint.sh
RUN echo "mamba run --no-capture-output -n streamlit-env streamlit run app.py" >> /app/entrypoint.sh
# make the script executable
RUN chmod +x /app/entrypoint.sh
# Patch Analytics
RUN mamba run -n streamlit-env python hooks/hook-analytics.py
# Set Online Deployment
RUN jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json
# Download latest OpenMS App executable for Windows from Github actions workflow.
RUN WORKFLOW_ID=$(curl -s "https://api.github.com/repos/$GITHUB_USER/$GITHUB_REPO/actions/workflows" | jq -r '.workflows[] | select(.name == "Build executable for Windows") | .id') \
&& SUCCESSFUL_RUNS=$(curl -s "https://api.github.com/repos/$GITHUB_USER/$GITHUB_REPO/actions/runs?workflow_id=$WORKFLOW_ID&status=success" | jq -r '.workflow_runs[0].id') \
&& ARTIFACT_ID=$(curl -s "https://api.github.com/repos/$GITHUB_USER/$GITHUB_REPO/actions/runs/$SUCCESSFUL_RUNS/artifacts" | jq -r '.artifacts[] | select(.name == "OpenMS-App") | .id') \
&& curl -LJO -H "Authorization: Bearer $GITHUB_TOKEN" "https://api.github.com/repos/$GITHUB_USER/$GITHUB_REPO/actions/artifacts/$ARTIFACT_ID/zip" -o /app/OpenMS-App
# make sure that mamba environment is used
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
EXPOSE $PORT
ENTRYPOINT ["/app/entrypoint.sh"]