docker simplified

Dockerfile

@@ -43,101 +43,17 @@ ENV RETICULATE_PYTHON_ENV=/home/env \
     ENV_VARS=WANDB_ENTITY,WANDB_PROJECT,USER_NAME,USER_ID,GROUP_ID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES\
     HOME="/home/"
 
-RUN echo "---> RETICULATE PYTHONS"
-RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
-RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron
-
-
-ENV MINICONDA_VERSION=4.10.3 \ 
-#ENV MINICONDA_VERSION=23.9.0 \ 
-    CONDA_DIR=$HOME/miniconda3 \
-    # Make non-activate conda commands available
-    PATH=$CONDA_DIR/bin:$PATH \
-    PROJECT_DIR=$HOME 
-
-RUN echo "HOME: ${HOME} | CONDA_DIR = ${CONDA_DIR}" \
-    #-- Install MINICONDA
-    && wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh  \
-    && chmod +x ~/miniconda.sh  \
-    && ~/miniconda.sh -b -p $CONDA_DIR  \
-    && rm ~/miniconda.sh 
-
-    # Make conda activate command available from /bin/bash --login shells
-RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> $HOME/.profile 
-    # make conda activate command available from /bin/bash --interative shells
-RUN  conda init bash \
-    # create a project directory inside user home
-    && mkdir -p $PROJECT_DIR
-
-
-WORKDIR $PROJECT_DIR
-##########################
-# Install & update MAMBA #
-########################## 
-ENV ENV_PREFIX $PROJECT_DIR/env
-RUN conda install --name base --channel conda-forge mamba \
-    && mamba update --name base --channel defaults conda 
-#-- Build the mamba environment
-RUN mamba install conda-lock -c conda-forge
-COPY --chown=$UID:$GID docker/environment.yml docker/requirements.txt /tmp/
-#RUN mamba lock -f /tmp/environment.yml --lockfile /tmp/environment.lock
-#RUN mamba create --prefix ${ENV_PREFIX} --file /tmp/environment.lock
-RUN mamba env create -vv --prefix ${ENV_PREFIX} --file /tmp/environment.yml
-RUN conda clean --all --yes
-
-# run the postBuild script to install the JupyterLab extensions
-COPY --chown=$UID:$GID docker/postBuild /usr/local/bin
-RUN chmod u+x /usr/local/bin/postBuild \
-    && conda activate $ENV_PREFIX  \
-    && /usr/local/bin/postBuild  \
-    && conda deactivate \
-    # Make bash automatically activate the conda environment
-    && echo "conda activate $ENV_PREFIX" >> ~/.bashrc
-
-
-RUN chmod u+x /usr/local/bin/postBuild \
-    && conda activate $ENV_PREFIX  \
-    && /usr/local/bin/postBuild  \
-    && conda deactivate \
-    # Make bash automatically activate the conda environment
-    && echo "conda activate $ENV_PREFIX" >> ~/.bashrc
-
-RUN conda list --prefix ${ENV_PREFIX}
-
-RUN echo "--> rewrrite miniconda path"
-# Rewrite the miniconda path environment in case it has been redefined in the compose file
-RUN echo "RETICULATE_MINICONDA_PATH=${RETICULATE_MINICONDA_PATH}" >> ${HOME}/.Renviron
-
-RUN echo "---> Make non-activate conda commands available"
-RUN # make non-activate conda commands available
-ENV PATH=${RETICULATE_MINICONDA_PATH}/bin:${PATH}
-RUN echo "--> Permissions"
-
-RUN echo "$(id )"
 
 ### Copy deepvats
-RUN echo "---> Setup volumes" \
-    echo ${HOME} \
-    echo ${USER_NAME}"|"${USER_ID}"|"${GROUP_ID} 
-
-COPY --chown=${USER_ID}:${GROUP_ID} ../r_shiny_app $HOME/app
-COPY --chown=${USER_ID}:${GROUP_ID} ${LOCAL_DATA_PATH} $HOME/data/
-COPY --chown=${USER_ID}:${GROUP_ID} ../dvats ${HOME}/dvats
-
-
-# Define an array of environment variable names from the ENV_VARS Compose variable
-#ARG ENV_VARS=ENV_VARS
-#RUN echo "---> Setup variables" && \
-#    IFS=',' read -ra NAMES <<< "ENV_VARS" && \
-#    for ENV_VAR_NAsME in "${NAMES[@]}"; do \ 
-    #echo "$ENV_VARS" | tr ',' '\n' | while read ENV_VAR_NAME; do \
-#    ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}"; \
-#    echo "$ENV_VAR_NAME=$ENV_VAR_VALUE"; \
-#    done > ${HOME}/.Renviron
+RUN echo "---> Setup volumes" 
+#--- Volumes
+COPY --chown=${USER_ID}:${GROUP_ID} ../r_shiny_app $HOME/${USER_NAME}app
+COPY --chown=${USER_ID}:${GROUP_ID} ${LOCAL_DATA_PATH} $HOME/${USER_NAME}data/
+COPY --chown=${USER_ID}:${GROUP_ID} ../dvats ${HOME}/${USER_NAME}/dvats
 
 # Install deepvats
 
-RUN pip install -e  /home/${USER_NAME}/work
+RUN pip install -e  /home/work
 RUN echo "--> Go!"
 
 CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=${RSTUDIO_PORT:-3838}, launch.browser = FALSE, appDir = '/home/${USER_NAME}/app')"]