changed: base image to base-notebook:latest

Author: flemk

Dockerfile

@@ -1,23 +1,29 @@
-# Jupyter container used for Galaxy IPython (+other kernels) Integration
+FROM quay.io/jupyter/base-notebook:latest
 
-# We want to support Python, R, Julia, Bash and to a lesser degree ansible, octave
-# https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html
-# Accoring to the link above we should take scipy-notebook and add additional kernels.
-# Since Julia installation seems to be complicated we will take the Julia notebook as base and install separate kernels into separate envs
-FROM quay.io/jupyter/julia-notebook:python-3.12
-
-LABEL org.opencontainers.image.authors="Björn A. Grüning, bjoern.gruening@gmail.com"
+LABEL org.opencontainers.image.source=https://github.com/IMTEK-Simulation/Docker4Teching
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-# Set channels to bioconda > conda-forge
+EXPOSE 8888
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential gcc g++ gfortran liblapack-dev libblas-dev \
+    git wget curl ca-certificates libglu1-mesa-dev libgmp-dev unixodbc-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+SHELL ["/bin/bash", "-lc"]
+
 RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
+    conda install -y mamba -n base -c conda-forge && \
     conda --version
 
-# Install python and jupyter packages
-RUN conda install --yes \ 
+RUN mamba install -y \
     bioblend galaxy-ie-helpers \
     biopython \
     cloudpickle \
@@ -35,100 +41,23 @@ RUN conda install --yes \
     pyvista \
     python-gmsh \
     statsmodels && \
-    conda create -n bash-kernel --yes bash_kernel=0.10.0 bioblend galaxy-ie-helpers && \
+    mamba clean --all -y
+
+RUN mamba create -y -n bash-kernel bash_kernel=0.10.0 bioblend galaxy-ie-helpers && \
     conda run -n bash-kernel python -m bash_kernel.install --user && \
-    conda create -n ansible-kernel --yes ansible-kernel=1.0.0 jupyter_client bioblend galaxy-ie-helpers && \
+    mamba create -y -n ansible-kernel ansible-kernel=1.0.0 jupyter_client bioblend galaxy-ie-helpers && \
     conda run -n ansible-kernel python -m ansible_kernel.install && \
-    conda create -n octave-kernel --yes python=3.8 octave_kernel=0.36.0 bioblend galaxy-ie-helpers && \
+    mamba create -y -n octave-kernel python=3.8 octave_kernel=0.36.0 bioblend galaxy-ie-helpers && \
     conda run -n octave-kernel python -m octave_kernel install --user && \
-    conda create -n rlang-kernel --yes r-base r-irkernel=1.3.2 r-xml rpy2 bioblend galaxy-ie-helpers \
-    	    'r-caret' \
-	    'r-crayon' \
-	    'r-devtools' \
-	    'r-e1071' \
-	    'r-forecast' \
-	    'r-hexbin' \
-	    'r-htmltools' \
-	    'r-htmlwidgets' \
-	    'r-irkernel' \
-	    'r-nycflights13' \
-	    'r-randomforest' \
-	    'r-rcurl' \
-	    'r-rmarkdown' \
-	    'r-rodbc' \
-	    'r-rsqlite' \
-	    'r-shiny' \
-	    'r-tidymodels' \
-	    'r-tidyverse' \
-	    'unixodbc' && \
+    mamba create -y -n rlang-kernel r-base r-irkernel=1.3.2 r-xml rpy2 bioblend galaxy-ie-helpers \
+        r-caret r-crayon r-devtools r-e1071 r-forecast r-hexbin r-htmltools r-htmlwidgets \
+        r-irkernel r-nycflights13 r-randomforest r-rcurl r-rmarkdown r-rodbc r-rsqlite r-shiny \
+        r-tidymodels r-tidyverse unixodbc && \
     conda run -n rlang-kernel R -e "IRkernel::installspec(user = TRUE, name = 'rlang-kernel', displayname = 'R')" && \
-    conda clean --all -y && \
-    chmod a+w+r /opt/conda/ -R
-
-RUN echo 'Sys.setenv(CONDA_PREFIX = "/opt/conda/envs/rlang-kernel")' >> /home/$NB_USER/.Rprofile && \
-    echo 'Sys.setenv(PATH = paste("/opt/conda/envs/rlang-kernel/bin", Sys.getenv("PATH"), sep=":"))' >> /home/$NB_USER/.Rprofile && \
-    echo 'Sys.setenv(PROJ_LIB = "/opt/conda/envs/rlang-kernel/share/proj")' >> /home/$NB_USER/.Rprofile && \
-    chown $NB_USER /home/$NB_USER/.Rprofile
-
-ADD ./startup.sh /startup.sh
-#ADD ./monitor_traffic.sh /monitor_traffic.sh
-ADD ./get_notebook.py /get_notebook.py
-
-# We can get away with just creating this single file and Jupyter will create the rest of the
-# profile for us.
-RUN mkdir -p /home/$NB_USER/.ipython/profile_default/startup/ && \
-    mkdir -p /home/$NB_USER/.jupyter/custom/
-
-ADD ./ipython-profile.py /home/$NB_USER/.ipython/profile_default/startup/00-load.py
-ADD jupyter_notebook_config.py /home/$NB_USER/.jupyter/
-ADD jupyter_lab_config.py /home/$NB_USER/.jupyter/
-
-ADD ./custom.js /home/$NB_USER/.jupyter/custom/custom.js
-ADD ./custom.css /home/$NB_USER/.jupyter/custom/custom.css
-ADD ./default_notebook.ipynb /home/$NB_USER/notebook.ipynb
-
-# ENV variables to replace conf file
-ENV DEBUG=false \
-    GALAXY_WEB_PORT=10000 \
-    NOTEBOOK_PASSWORD=none \
-    CORS_ORIGIN=none \
-    DOCKER_PORT=none \
-    API_KEY=none \
-    HISTORY_ID=none \
-    REMOTE_HOST=none \
-    GALAXY_URL=none
-
-# @jupyterlab/google-drive  not yet supported
+    mamba clean --all -y
 
 USER root
 
-# R pre-requisites
-RUN apt-get update --yes && \
-    apt-get install --yes --no-install-recommends \
-    fonts-dejavu \
-    unixodbc \
-    unixodbc-dev \
-    r-cran-rodbc \
-    gfortran \
-    net-tools \
-    procps \
-    libgl1 \
-    xvfb \
-    gcc && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
-
-# /import will be the universal mount-point for Jupyter
-# The Galaxy instance can copy in data that needs to be present to the Jupyter webserver
-RUN mkdir -p /import/jupyter/outputs/ && \
-    mkdir -p /import/jupyter/data && \
-    mkdir -p /import/jupyter/mount && \
-    mkdir /export/ && \
-    chown -R $NB_USER:users /home/$NB_USER/ /import /export/ && \
-    chmod -R 777 /home/$NB_USER/ /import /export/
-
-##USER jovyan
-
-WORKDIR /import
+RUN chmod -R a+rw /opt/conda && chown -R ${NB_UID}:${NB_GID} /home/jovyan
 
-# Start Jupyter Notebook
-CMD /startup.sh
+USER $NB_UID