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#############################
# RSTUDIO-SERVER #
# VOLUME DOCKERFILE #
#***************************#
# Set up a jupyter-lab for #
# developing using deepvats #
#############################
##############
# Base image #
##############
# Adds rstudio server, tiyverse, devtools to rocker/cuda
FROM rocker/ml:4.2
SHELL [ "/bin/bash", "--login", "-c" ]
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC
RUN apt-get update
RUN apt-get install -y python3-pip
RUN python3 -m pip install --upgrade pip
RUN apt-get install -y python3-venv libxt-dev
## Install R packages
#COPY docker/DESCRIPTION /tmp/
COPY --chown=${UID}:${GID} docker/DESCRIPTION /tmp/
RUN ls -la /tmp/ && sleep 5
#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 HOME /home/
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}" >> /${HOME}/.Renviron
COPY docker/entrypoint-rstudio.sh /usr/local/bin
RUN chmod u+x /usr/local/bin/entrypoint-rstudio.sh
ENTRYPOINT [ "/usr/local/bin/entrypoint-rstudio.sh" ]
RUN echo "--> rewruie miniconda path"
# Rewrite the miniconda path environment in case it has been redefined in the compose file
RUN echo "RETICULATE_MINICONDA_PATH=${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 miniconda3"
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}" >> ${HOME}/.Renviron
# Define an array of environment variable names from the ENV_VARS Compose variable
RUN echo "---> Setup variables"
RUN IFS=',' read -ra ENV_VAR_NAMES <<< "$ENV_VARS"
RUN echo "ENV_VAR_NAMES=${ENV_VAR_NAMES[@]}"
# Loop through the array of environment variable names and set the variables
RUN for ENV_VAR_NAME in "${ENV_VAR_NAMES[@]}"; do \
ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}" \
echo "$ENV_VAR_NAME=$ENV_VAR_VALUE" >> ${HOME}/rstudio/.Renviron \
done
RUN echo "--> Go!"
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