Dockerfile

FROM jupyter/tensorflow-notebook:python-3.8.8

USER root

# Install ETHZ root ca certificates
ADD http://pkiaia.ethz.ch/aia/ETHZRootCA2020.pem /usr/local/share/ca-certificates/ETHZRootCA2020.crt
ADD http://pkiaia.ethz.ch/aia/ETHZIssuingCA2020.pem /usr/local/share/ca-certificates/ETHZIssuingCA2020.crt
ADD http://pkiaia.ethz.ch/aia/DigiCertGlobalRootCA.pem /usr/local/share/ca-certificates/DigiCertGlobalRootCA.crt
ADD http://pkiaia.ethz.ch/aia/DigiCertTLSRSASHA2562020CA1-1.pem /usr/local/share/ca-certificates/DigiCertTLSRSASHA2562020CA1-1.crt
RUN chmod 644 /usr/local/share/ca-certificates/* && update-ca-certificates

RUN apt-get update && apt-get upgrade -y && apt-get install -y zip && \
    # Make conda writeable for the user
    chown -R 1000 /opt/conda

# Install QIIME 2 with all its dependencies
COPY qiime2-2022.2-py38-linux-conda.yml .
RUN mamba env update -n base --file qiime2-2022.2-py38-linux-conda.yml && \
    rm qiime2-2022.2-py38-linux-conda.yml && \
    jupyter serverextension enable --py qiime2 --sys-prefix && \
    qiime dev refresh-cache

# Install some JLab goodies and other packages
RUN mamba install -c conda-forge \
    jupyterlab-system-monitor jupyterlab-git \
    uncertainties nbgrader pylatex biopython ete3 nbgitpuller

RUN conda init bash && \
    source $HOME/.bashrc

USER 1000