Unverified Commit c7e6ad62 authored by Michal Ziemski's avatar Michal Ziemski
Browse files

Enable env creation by the user. Clean up the image.

parent 1689e237
Pipeline #138097 passed with stages
in 23 minutes and 56 seconds
......@@ -9,20 +9,20 @@ ADD http://pkiaia.ethz.ch/aia/DigiCertGlobalRootCA.pem /usr/local/share/ca-certi
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
RUN apt-get update && apt-get upgrade -y && apt-get install -y zip && \
# Make conda writeable for the user
chown -R 1000 /opt/conda
#RUN wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
# 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
RUN rm qiime2-2022.2-py38-linux-conda.yml
RUN qiime dev refresh-cache
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
# This could later be combined with the step below?
RUN mamba install -c conda-forge jupyterlab-system-monitor jupyterlab-git
# Our standard notebook gets this. Remove if you encounter conflicts or other issues
# Removing scikit-learn, keras as they were installed above. Also, moving this
# step to the end as otherwise mamba fails to resolve some deps.
RUN mamba install uncertainties nbgrader pylatex biopython ete3 nbgitpuller
# Install some JLab goodies and other packages
RUN mamba install -c conda-forge \
jupyterlab-system-monitor jupyterlab-git \
uncertainties nbgrader pylatex biopython ete3 nbgitpuller
USER 1000
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