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Dockerfile
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# TODO: Use a more specific tag instead of latest for reproducibility
FROM ubuntu:latest
ENV DEBIAN_FRONTEND=noninteractive
# XVFB_RES="1920x1080x24" \
# XVFB_ARGS="" \
# PATH="/app/.venv/bin:$PATH" \
# CONFIG_ENV_FILE="/app/config/config.env" \
# SECRET_ENV_FILE="/app/secret/secret.env" \
# STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
# STORAGE_LOCAL_CACHE_DIR="/app/scratch"
WORKDIR /app
# copy and make dirs
COPY ./biosimulator_processes /app/biosimulator_processes
COPY notebooks /app/notebooks
# copy files
COPY pyproject.toml poetry.lock ./data ./scripts/trust-notebooks.sh /app/
# COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
VOLUME /app/data
RUN apt-get update && apt-get install -y --no-install-recommends \
python3.10 \
ca-certificates \
python3-pip \
python3-dev \
build-essential \
libncurses5 \
cmake \
make \
libx11-dev \
libc6-dev \
libx11-6 \
libc6 \
gcc \
swig \
pkg-config \
curl \
tar \
libgl1-mesa-glx \
libice6 \
libpython3.10 \
wget \
&& rm -rf /var/lib/apt/lists/* \
&& pip install --upgrade pip && pip install poetry \
&& poetry config virtualenvs.in-project true \
&& poetry update \
&& poetry install \
&& chmod +x ./trust-notebooks.sh \
&& ./trust-notebooks.sh \
&& rm ./trust-notebooks.sh \
&& apt-get clean \
&& apt-get autoclean
# CMD ["poetry", "run", "jupyter", "lab", "--port=8888", "--no-browser", "--allow-root"]
# PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle
# such logic in conversion on the HPC.
# type imports
# dist
# param scan demo/location