getdemo / Dockerfile-dockerhub
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# This is the dockerfile for dockerhub fuxialexander/getdemo:latest
FROM mambaorg/micromamba
USER root
RUN usermod -u 1000 $MAMBA_USER
USER $MAMBA_USER
# Set the working directory in the container to /app
WORKDIR /app
# Create a new environment using mamba with specified packages
RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 pip biopython s3fs
RUN micromamba install -n base -c conda-forge -c bioconda -y nglview tqdm matplotlib pandas
RUN micromamba install -n base -c conda-forge -c bioconda -y openpyxl pyarrow python-box xmlschema seaborn numpy py3Dmol pyranges scipy pyyaml zarr numcodecs
RUN micromamba install -n base -c conda-forge -c bioconda -y pybigwig networkx plotly pysam requests seqlogo MOODS urllib3 pyliftover gprofiler-official pyfaidx
RUN micromamba install -n base -c conda-forge -y dash-bio
ARG MAMBA_DOCKERFILE_ACTIVATE=1
# Activate the environment and install additional packages via pip
RUN pip3 install gradio
USER root
RUN mkdir /data
RUN apt-get update && apt-get install -y --no-install-recommends \
git \
ssh \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
USER $MAMBA_USER
# copy modules from local to container
COPY --chown=$MAMBA_USER:$MAMBA_USER modules /app/modules
# copy modules from local to container
COPY --chown=$MAMBA_USER:$MAMBA_USER app /app/app
# copy modules from local to container
# COPY --chown=$MAMBA_USER:$MAMBA_USER data /app/data
# Clone a specific git repository and install it as an editable package
RUN cd modules/proscope && \
pip3 install .
RUN cd modules/atac_rna_data_processing && \
pip3 install .
# clean all mamba caches and remove unnecessary files
RUN micromamba clean --all --yes
WORKDIR /app
# Make port 80 available to the world outside this container
EXPOSE 7860
# Set the working directory where your app resides
# Command to run the Gradio app automatically
CMD ["python", "app/main.py", "-p", "7860", "-s", "-u", "s3://2023-get-xf2217/get_demo", "-d", "/data"]