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# read the doc: https://huggingface.co/docs/hub/spaces-sdks-docker
# you will also find guides on how best to write your Dockerfile
FROM continuumio/miniconda3:latest
# Add build argument to force rebuild
ARG CACHEBUST=1
# Avoid tzdata interactive configuration
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=UTC
# Install system dependencies
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
git \
build-essential \
python3-dev \
wget \
openmpi-bin \
libopenmpi-dev \
libopenmpi3 \
libhwloc15 \
libevent-dev \
libpmix2 \
libgl1 \
libglib2.0-0 \
&& rm -rf /var/lib/apt/lists/*
# Set up OpenMPI environment
ENV OMPI_MCA_btl_vader_single_copy_mechanism=none \
OMPI_ALLOW_RUN_AS_ROOT=1 \
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
PATH=/usr/lib/x86_64-linux-gnu/openmpi/bin:$PATH \
LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/openmpi/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
# Copy environment file
COPY colabs/environment.yml /tmp/environment.yml
# Create conda environment
RUN conda env create -f /tmp/environment.yml && \
conda run -n biomedparse pip install gradio==3.50.2
# Initialize conda in bash
RUN conda init bash
# Make RUN commands use the new environment
SHELL ["conda", "run", "-n", "biomedparse", "/bin/bash", "-c"]
# Set up a new user named "user" with user ID 1000
RUN useradd -m -u 1000 user
# Switch to the "user" user
USER user
# Set up HF token for the user
RUN --mount=type=secret,id=HF_TOKEN,mode=0444,required=true \
echo "export HF_TOKEN=$(cat /run/secrets/HF_TOKEN)" >> $HOME/.bashrc
# Set home to the user's home directory
ENV HOME=/home/user \
PATH=/home/user/.local/bin:$PATH
# Set the working directory to the user's home directory
WORKDIR $HOME/app
# Copy all files to the app directory
COPY --chown=user . $HOME/app
# Set permissions for entrypoint script
RUN chmod 755 $HOME/app/entrypoint.sh
# Add conda environment to user's path
RUN echo "conda activate biomedparse" >> $HOME/.bashrc
# Use entrypoint script to set up environment and run application
ENTRYPOINT ["/bin/bash", "-c"]
CMD ["exec /home/user/app/entrypoint.sh"]
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