Upgrade binder submodule, use fully pinned environment definition #4
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alimanfoo
commented
Jul 18, 2019
| && apt-get clean \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| USER $NB_USER | ||
| RUN conda config --set ssl_verify no | ||
| COPY binder/environment.yml /tmp/environment.yml | ||
| COPY binder/environment-pinned-linux.yml /tmp/environment.yml |
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This is the main change, using the fully pinned environment file.
| RUN conda config --add channels bioconda | ||
| RUN conda config --add channels conda-forge | ||
| #RUN conda update --yes conda | ||
| RUN conda config --set channel_priority strict |
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This is also an important change, ensures packages are pulled from conda-forge instead of defaults wherever possible, which results in a more consistent environment.
| RUN conda config --add channels bioconda | ||
| RUN conda config --add channels conda-forge | ||
| #RUN conda update --yes conda | ||
| RUN conda config --set channel_priority strict | ||
| RUN conda update --yes conda |
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I saw this had been commented out, but there have been some improvements in recent conda versions, so thought maybe best to run it?
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| RUN conda env update --file /tmp/environment.yml --prune | ||
| RUN conda env update --file /tmp/environment.yml |
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We are installing this into the base environment, is that right?
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I.e., I think the environment name from within the environment file will be ignored.
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This PR upgrades the binder submodule, which now provisions a fully pinned conda environment definition file, including all dependency packages (see malariagen/mgenv#52 for further details).