Dockerfile

#R-Shiny template https://huggingface.co/spaces/posit/shiny-for-r-template/tree/main
#Py-shiny template https://huggingface.co/spaces/posit/gptneox-chat

#############################
# RSTUDIO-SERVER            #
# VOLUME DOCKERFILE         #
#***************************#
# Set up a jupyter-lab for  #
# developing using deepvats #
#############################

##############
# Base image #
##############
# Adds rstudio server, tiyverse, devtools to rocker/cuda
FROM dvats-rstudio-base:latest

RUN echo "--> Prior installations" \ 
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC \
    set -e; \
    apt-get update --fix-missing \
    && apt-get install -y \
    python3-pip wget bzip2 curl \
    git sudo libarchive-dev libtiff5-dev zsh\
    #python3 -m pip install --upgrade pip \
    python3-venv libxt-dev \
    && apt-get clean  \
    && rm -rf /var/lib/apt/lists/* 


SHELL [ "/bin/bash", "--login", "-c" ]

###############
# Ensure vars # (Only for local test - DON'T USE IT IN HUGGINGFACE. ENSURE .env IS NOT ACCESIBLE IN THE WEB, USE THEIR SECRET MANAGEMENT)
###############
RUN echo "--> ARGS"
ARG USER_NAME=user \
    USER_ID=1000 \
    GROUP_ID \
    WANDB_API_KEY \ 
    WANDB_ENTITY \
    WANDB_PROJECT \
    GH_TOKEN 

RUN echo "--> ARGS -> ENV"
ENV USER_NAME=$USER_NAME \
    USER_ID=$USER_ID \
    GROUP_ID=$GROUP_ID \
    WANDB_ENTITY=$WANDB_ENTITY \
    WANDB_API_KEY=$WANDB_API_KEY \
    GH_TOKEN=$ghtoken \
    WANDB_PROJECT=$WANDB_PROJECT

RUN echo "--> Setup ENV variables"
ENV RETICULATE_PYTHON_ENV=/home/${USER_NAME}/env \
    ROOT=TRUE \
    RETICULATE_MINICONDA_PATH=/home/${USER_NAME}/miniconda \
    CUDA_VISIBLE_DEVICES=0,1,2 \
    ENV_VARS=WANDB_ENTITY,WANDB_PROJECT,USER_NAME,USER_ID,GROUP_ID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES\
    HOME="/home/${USER_NAME}"

###########
# Volumes #
###########




## Install R packages

# COPY docker/DESCRIPTION /tmp/
COPY --chown=${USER_ID}:${GROUP_ID} docker/DESCRIPTION /tmp/

RUN echo "--> Install R packages" \ 
    R -e "devtools::install_deps('/tmp/', dependencies = TRUE)"

## Reticulate configuration
ENV ENV_PREFIX $HOME/env

RUN echo "---> Make sudo & setup sudoers"
RUN echo "$(id)"

ARG RETICULATE_MINICONDA_PATH=/usr/local/share/r-miniconda
ARG RETICULATE_PYTHON_ENV=/usr/virtualenvs/venv_shiny_app
ENV RETICULATE_PYTHON=${RETICULATE_PYTHON_ENV}/bin/python/

RUN echo "---> RETICULATE PYTHONS"
RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron

RUN echo "---> Export W&B"
## Export W&B environment variable to Rstudio

ARG WANDB_API_KEY
RUN echo "WANDB_API_KEY=${WANDB_API_KEY}" >> ${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

#RUN echo "--> Setup miniconda & Mamba"

#RUN echo ". ${HOME}miniconda3/etc/profile.d/conda.sh" >> ${HOME}/rstudio/.bashrc


#RUN echo "--> Conda activate"
# Make bash automatically activate the conda environment
#RUN echo "conda activate ${ENV_PREFIX}" >> ${HOME}/rstudio/.bashrc
#echo "export WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.bashrc
# echo "WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.Renviron

# 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

# Install deepvats

RUN pip install -e  /home/${USER_NAME}/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')"]

# CMD ["/init"]