Dockerfile

# Use the official Anaconda base image
FROM continuumio/anaconda3@sha256:bd2af590d39a5d1b590cd6ad2abab37ae386b7e2a9b9d91e110d3d82074f3af9

# Set environment variable to avoid user interaction during package installation
ENV DEBIAN_FRONTEND=noninteractive

# Update current packages and install some useful tools. libgl1-mesa-glx necessary for spyder
RUN apt-get update && \
    apt-get install -y \
    libgl1-mesa-glx \
    less \
    nano \
    && apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN useradd -ms /bin/bash clarkad

# Create the spyder environment to run out of. The container will start with this environment active, but you can switch to a different kernel inside spyder and have it run without issue
ADD ./envs/spyder_env.yml /tmp/spyder_env.yml
RUN conda env create -y -f /tmp/spyder_env.yml

# Create the cellxgene environment based on an environment file. 
ADD ./envs/cellxgene.txt /tmp/cellxgene.txt
RUN conda create -y --name cellxgene --file /tmp/cellxgene.txt

SHELL ["bash"]
ENTRYPOINT [ "conda", "run", "--no-capture-output", "-p", "/opt/conda/envs/spyder-env", "spyder" ]