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#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
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_ID \
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 #
###########
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 ${HOME}/dvats
RUN echo "--> Prior installations" \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC \
set -e; \
apt-get update --fix-missing \
&& apt-get install -y \
python3-pip wget bzip2 curl \
git sudo libarchive-dev libtiff5-dev zsh\
#python3 -m pip install --upgrade pip \
python3-venv libxt-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
## Install R packages
#COPY docker/DESCRIPTION /tmp/
COPY --chown=${USER_ID}:${GROUP_ID} docker/DESCRIPTION /tmp/
RUN ls -la /tmp/ && sleep 5
RUN echo "--> Install R packages"
#RUN R -e "install.packages(deps_path = '/tmp/DESCRIPTION', remotes::dev_package_deps(dependencies = TRUE), repos = NULL)"
RUN R -e "devtools::install_deps('/tmp/', dependencies = TRUE)"
#RUN R -e "install.packages(c('shiny', 'pals', 'shinyWidgets', 'dygraphs', 'shinycssloaders', 'shinyjs', 'Rcpp', 'reactlog', 'pals', 'feather', 'fasttime', 'zoo', 'shinyWidgets'))"
#RUN R -e "remotes::install_github('r-lib/later')"
#RUN R -e "remotes::install_github('apache/arrow/r')"
## Install reticulate and create virtual environment using default Ubuntu installed Python
#RUN R -e "install.packages('reticulate')"
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" >> ~/.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 )"
#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 > ${HOME}/.Renviron
RUN echo "--> Go!"
CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=${RSTUDIO_PORT:-3838}, launch.browser = FALSE, appDir = '/home/${USER_NAME}/app')"]
# CMD ["/init"]
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