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HopkinsIDD · Oct 17, 2023 · a4c19d6 · a4c19d6
1 parent 3afed8c
commit a4c19d6
Showing 1 changed file with 137 additions and 0 deletions.
diff --git a/Dockerfile.nxt b/Dockerfile.nxt
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+FROM ubuntu:20.04
+
+USER root
+ENV TERM linux
+
+# set locale info
+RUN apt-get update && apt-get install -y locales && locale-gen en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+ENV R_VERSION 4.2.2.20221110-1.2004.0
+
+# set noninteractive installation
+ENV DEBIAN_FRONTEND noninteractive
+
+# see https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04
+# https://cran.r-project.org/bin/linux/debian/
+# https://cran.r-project.org/bin/linux/ubuntu/README.html
+RUN set -e \
+      && apt-get update \
+      && apt-get -y install --no-install-recommends --no-install-suggests \
+        gnupg2 gnupg1 ca-certificates software-properties-common \
+      && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+      && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
+      && add-apt-repository ppa:git-core/ppa
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    # needed packages
+    tzdata \
+    sudo \
+    less \
+    build-essential \
+    git-core \
+    git-lfs \
+    curl \
+    pandoc \
+    pandoc-citeproc \
+    postgresql-client \
+    libpq-dev \
+    libssl-dev \
+    openssl \
+    libgdal-dev \
+    libyaml-dev \
+    libjpeg-dev \
+    libxml2-dev \
+    libxslt1-dev \
+    libffi-dev \
+    libblas-dev \
+    liblapack-dev \
+    libatlas-base-dev \
+    libxml2-dev \
+    libcurl4-openssl-dev \
+    libfontconfig1-dev \
+    libcairo2-dev \
+    libudunits2-dev \
+    gfortran \
+    unzip \
+    zip \
+    pbzip2 \
+    vim-nox \
+    nano \
+    libbz2-dev \
+    libsqlite3-dev \
+    sqlite3 \
+    openssh-server \
+    libsnappy-dev \
+    libncurses-dev \
+    libreadline-dev \
+    # add for debug
+    libxt-dev \
+    # for rstan
+    libv8-dev \
+    # for gdal
+    gdal-bin \
+    supervisor \
+    awscli \
+    r-base-core=$R_VERSION \
+    postgresql \
+    postgis \
+    postgresql-12-postgis-3 \
+    # make sure we have up-to-date CA certs or curling some https endpoints (like python.org) may fail
+    ca-certificates \
+    # app user creation
+    && useradd -m app \
+    && mkdir -p /home/app \
+    && chown -R app:app /home/app \
+    # set up sudo for app user
+    && sudo echo "app ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/app \
+    && sudo usermod -a -G staff app
+
+WORKDIR /home/app
+USER app
+ENV HOME /home/app
+
+####
+# POSTGIS
+####
+# TODO: Set up postgis database
+COPY --chown=app:app grant_cholera_database.sh $HOME/grant_cholera_database.sh
+RUN sudo service postgresql start \
+    && sudo -u postgres psql -c "CREATE DATABASE cholera_covariates;" \
+    && sudo -u postgres psql -c "CREATE USER app WITH LOGIN;" \
+    && sudo -u postgres psql -c "GRANT ALL ON DATABASE cholera_covariates TO app;" \
+    && sudo -u postgres psql -d cholera_covariates -c "CREATE EXTENSION postgis;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION postgis_raster;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION postgis_topology;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION postgis_sfcgal;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION fuzzystrmatch;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION address_standardizer;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION address_standardizer_data_us;" \
+    && sudo -u postgres psql -d  cholera_covariates -c "CREATE EXTENSION postgis_tiger_geocoder;" \
+    && sudo -u app psql -d  cholera_covariates -c "CREATE SCHEMA covariates;" \
+    && sudo -u app psql -d  cholera_covariates -c "CREATE SCHEMA data;" \
+    && sudo -u app psql -d  cholera_covariates -c "CREATE SCHEMA grids;" \
+    # && /bin/bash grant_cholera_database.sh app\
+    && /bin/bash -c "/usr/bin/echo 'sudo service postgresql start' >> /home/app/.bashrc"
+
+#####
+# R
+#####
+
+RUN sudo Rscript -e "install.packages('renv',repos='https://cloud.r-project.org/')" \
+    && cd /home/app 
+    # && Rscript -e "renv::restore()"
+    # && Rscript -e "cmdstanr::install_cmdstan()"
+COPY --chown=app:app renv.cache $HOME/.cache
+COPY --chown=app:app renv.lock $HOME/renv.lock
+COPY --chown=app:app renv $HOME/renv
+RUN  sudo Rscript -e "options(renv.config.install.verbose=TRUE);renv::restore(lockfile='$HOME/renv.lock', library='$HOME/renv/library/R-4.2/x86_64-pc-linux-gnu')"
+COPY --chown=app:app Docker.Rprofile $HOME/.Rprofile
+
+RUN git clone https://www.github.com/stan-dev/cmdstan --recurse-submodules \
+  && cd cmdstan \
+  && make build
+
+CMD ["/bin/bash"]