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chore(jupyter-covid19): new base, non-root install (#41)
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| FROM quay.io/cdis/jupyter-nde-base:1.0.2 | ||
| USER root | ||
| FROM quay.io/cdis/jupyter-notebook:1.1.0 | ||
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| # copy welcome splash page | ||
| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/3.1.0/covid19-notebooks/welcome.html /home/jovyan/ | ||
| RUN touch /home/jovyan/welcome.html | ||
| USER $NB_USER | ||
| WORKDIR /home/$NB_USER | ||
| ARG COVID_TOOLS_BRANCH=master | ||
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| RUN chown -R jovyan:users /home/jovyan/welcome.html | ||
| # copy welcome splash page | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/3.1.0/covid19-notebooks/welcome.html /home/$NB_USER/ | ||
| RUN touch /home/$NB_USER/welcome.html | ||
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| # copy readme and notebooks requirements | ||
| RUN mkdir /home/jovyan/covid19-notebook | ||
| RUN mkdir /home/$NB_USER/covid19-notebook | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/readme.md /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/readme.md | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/readme.md /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/readme.md | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/requirements.txt /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/requirements.txt | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/requirements.txt /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/requirements.txt | ||
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| # copy premade notebooks | ||
| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/jhu-summary-overview/COVID-19-JHU_data_analysis.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/COVID-19-JHU_data_analysis.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/jhu-summary-overview/COVID-19-JHU_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/COVID-19-JHU_data_analysis.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/kaggle-demographics/kaggle_data_analysis.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/kaggle_data_analysis.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/kaggle-demographics/kaggle_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/kaggle_data_analysis.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/chicago-seir-forecast/covid19_seir.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/covid19_seir.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/covid19_seir.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/covid19_seir.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/chicago-seir-forecast/seir_diagram.png /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/seir_diagram.png | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/seir_diagram.png /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/seir_diagram.png | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/ctp_testing/CTP_testing.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/CTP_testing.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ctp_testing/CTP_testing.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/CTP_testing.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/TCGA_OV_COVID.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/TCGA_OV_COVID.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/TCGA_OV_COVID.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/TCGA_OV_COVID.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/symptoms_and_fatality_covid19.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/symptoms_and_fatality_covid19.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/symptoms_and_fatality_covid19.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/symptoms_and_fatality_covid19.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/SSR/SSR_notebook.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/SSR_notebook.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/SSR/SSR_notebook.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/SSR_notebook.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/X-ray/DarkCovidNet_binary_classes.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/DarkCovidNet_binary_classes.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/DarkCovidNet_binary_classes.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/DarkCovidNet_binary_classes.ipynb | ||
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| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/X-ray/DarkCovidNet_three_classes.ipynb /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/DarkCovidNet_three_classes.ipynb | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/DarkCovidNet_three_classes.ipynb /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/DarkCovidNet_three_classes.ipynb | ||
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| # peregrine helper script required by the X-ray notebooks | ||
| ADD https://raw.githubusercontent.com/uc-cdis/covid19-tools/master/covid19-notebooks/X-ray/peregrine.py /home/jovyan/covid19-notebook/ | ||
| RUN touch /home/jovyan/covid19-notebook/peregrine.py | ||
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| RUN chown -R jovyan:users /home/jovyan/covid19-notebook | ||
| ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/peregrine.py /home/$NB_USER/covid19-notebook/ | ||
| RUN touch /home/$NB_USER/covid19-notebook/peregrine.py | ||
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| # premade notebooks dependencies | ||
| RUN pip install --upgrade 'pip<20.3' # pip 20.3 causes dependency resolution issues | ||
| RUN pip install -r /home/jovyan/covid19-notebook/requirements.txt | ||
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| USER $NB_UID | ||
| WORKDIR /home/jovyan | ||
| RUN pip install -r /home/$NB_USER/covid19-notebook/requirements.txt |
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