Unverified Commit f05003c1 authored by Michal Ziemski's avatar Michal Ziemski
Browse files

Add QIIME 2 installation steps

Took 1 hour 50 minutes
parent 275d2f6a
Pipeline #137967 failed with stages
in 15 minutes and 56 seconds
......@@ -11,11 +11,13 @@ RUN chmod 644 /usr/local/share/ca-certificates/* && update-ca-certificates
RUN apt-get update && apt-get upgrade -y && apt-get install -y zip
# Our standard notebook gets this. Remove if you encounter conflicts or other issues
# RUN conda install uncertainties keras nbgrader scikit-learn nbgitpuller pylatex rise biopython ete3
RUN wget https://data.qiime2.org/distro/core/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
# Conda custom package installation
#
# RUN conda install <custom packages>
# Our standard notebook gets this. Remove if you encounter conflicts or other issues
# Removing scikit-learn, keras as they will be installed below. Also, moving this
# step to the end as otherwise mamba fails to resolve some deps.
RUN mamba install uncertainties nbgrader pylatex biopython ete3 nbgitpuller
USER 1000
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