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FROM jupyter/tensorflow-notebook:python-3.8.8
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USER root

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# 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

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#RUN wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
COPY qiime2-2022.2-py38-linux-conda.yml .
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RUN mamba env update -n base --file qiime2-2022.2-py38-linux-conda.yml
RUN rm qiime2-2022.2-py38-linux-conda.yml
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RUN qiime dev refresh-cache

# This could later be combined with the step below?
RUN mamba install -c conda-forge jupyterlab-system-monitor jupyterlab-git
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# Our standard notebook gets this. Remove if you encounter conflicts or other issues
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# Removing scikit-learn, keras as they were installed above. Also, moving this
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# step to the end as otherwise mamba fails to resolve some deps.
RUN mamba install uncertainties nbgrader pylatex biopython ete3 nbgitpuller
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USER 1000