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Dockerfile

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+#############################
+# RSTUDIO-SERVER            #
+# VOLUME DOCKERFILE         #
+#***************************#
+# Set up a jupyter-lab for  #
+# developing using deepvats #
+#############################
+##############
+# Base image #
+##############
+#FROM vrodriguezf/rstudio-server-shiny-development
+# 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')"
+
+ARG USER=user
+ARG UID=1000
+ARG GID=1000
+ENV HOME /home/$USER
+ENV ENV_PREFIX $HOME/env
+
+RUN addgroup --gid $GID $USER
+RUN adduser --disabled-password \
+    --gecos "Non-root user" \
+    --uid $UID \
+    --gid $GID \
+    --home $HOME \
+    $USER
+
+RUN adduser $USER sudo
+RUN echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+
+ARG RETICULATE_MINICONDA_PATH=/usr/local/share/r-miniconda
+ARG RETICULATE_PYTHON_ENV=/usr/virtualenvs/venv_shiny_app
+ENV RETICULATE_PYTHON=${RETICULATE_PYTHON_ENV}/bin/python/
+
+#RUN R -e "reticulate::virtualenv_create(envname='${RETICULATE_PYTHON_ENV}', python='/usr/bin/python3')"
+#RUN R -e "reticulate::virtualenv_install(c('numpy', 'pandas', 'wandb', 'hdbscan'), envname='${RETICULATE_PYTHON_ENV}')"
+
+RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
+RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron
+
+## Export W&B environment variable to Rstudio
+
+ARG WANDB_API_KEY
+RUN echo "WANDB_API_KEY=${WANDB_API_KEY}" >> /${HOME}/.Renviron
+
+# use an entrypoint script to insure conda environment is properly activated at runtime
+
+COPY --chown=${UID}:${GID} docker/entrypoint-rstudio.sh /usr/local/bin
+RUN chmod u+x /usr/local/bin/entrypoint-rstudio.sh
+ENTRYPOINT [ "/usr/local/bin/entrypoint-rstudio.sh" ]
+
+# Rewrite the miniconda path environment in case it has been redefined in the compose file
+RUN echo "RETICULATE_MINICONDA_PATH=${RETICULATE_MINICONDA_PATH}" >> ${HOME}/.Renviron
+
+# make non-activate conda commands available
+ENV PATH=${RETICULATE_MINICONDA_PATH}/bin:${PATH}