diff --git a/jupyter-covid19/Dockerfile b/jupyter-covid19/Dockerfile index cc9083ce..c77b32c5 100644 --- a/jupyter-covid19/Dockerfile +++ b/jupyter-covid19/Dockerfile @@ -1,98 +1,98 @@ -FROM quay.io/cdis/jupyter-notebook:restricted-download-1.3.0 +FROM quay.io/cdis/jupyter-notebook:restricted-download-1.3.1 USER $NB_USER WORKDIR /home/$NB_USER ARG COVID_TOOLS_BRANCH=master # copy welcome splash page -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/welcome.html /home/$NB_USER/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/welcome.html /home/$NB_USER/ RUN touch /home/$NB_USER/welcome.html # copy readme and notebooks requirements RUN mkdir /home/$NB_USER/covid19-notebook -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/readme.md /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/readme.md /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/readme.md -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/requirements.txt /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/requirements.txt /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/requirements.txt # copy premade notebooks -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/jhu-summary-overview/COVID-19-JHU_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/COVID-19-JHU_data_analysis.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/kaggle-demographics/kaggle_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/kaggle_data_analysis.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/covid19_seir.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/covid19_seir.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/seir_diagram.png /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/seir_diagram.png -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ctp_testing/CTP_testing.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/CTP_testing.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/TCGA_COAD_COVID.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/TCGA_COAD_COVID.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/TCGA_COAD_COVID.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/nCoV-2019_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/nCoV-2019_data_analysis.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/nCoV-2019_data_analysis.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/SSR/SSR_notebook.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/SSR_notebook.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/DarkCovidNet_binary_classes.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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/$NB_USER/covid19-notebook/DarkCovidNet_binary_classes.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/CNN_XRAY_CF.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/CNN_XRAY_CF.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/CNN_XRAY_CF.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/google_mobility.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/google_mobility.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/google_mobility.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/PFB_example.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/IL_tab_charts.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/IL_tab_charts.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/IL_tab_charts.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_gui.png /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_gui.png /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_7D4F_gui.png -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_view.html /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_view.html /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_7D4F_view.html -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_A_view.html /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_A_view.html /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_A_view.html -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_B_view.html /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_B_view.html /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_B_view.html -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_demo_view.html /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_demo_view.html /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_demo_view.html -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ICU_prediction/Percentage_ICU_prediction.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ICU_prediction/Percentage_ICU_prediction.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/Percentage_ICU_prediction.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir.ipynb /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir.ipynb /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/extended-seir.ipynb -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_diagram.png /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_diagram.png /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/extended-seir_diagram.png -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_parameters.png /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_parameters.png /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/extended-seir_parameters.png # small pfb file -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.avro /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.avro /home/$NB_USER/covid19-notebook/ RUN touch /home/$NB_USER/covid19-notebook/PFB_example.avro # peregrine helper script required by the X-ray notebooks -ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/peregrine.py /home/$NB_USER/covid19-notebook/ +ADD --chown=$NB_USER: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 # premade notebooks dependencies