install_pecan.sh

#!/bin/bash

set -e

if [ "`whoami`" == "root" ]; then
  echo "Don't run this script as root"
  exit -1
fi

# configuration
BROWNDOG_URL="http://dap.ncsa.illinois.edu:8184/convert/";
BROWNDOG_USERNAME="";
BROWNDOG_PASSWORD="";

SETUP_VM=""
SETUP_PALEON=""
REBUILD=""

PECAN_BRANCH="release/1.7.0"

DOCKER_COMPOSE="1.23.2"

RSTUDIO_SERVER="1.1.463"
SHINY_SERVER="1.5.9.923"

if [ -e $(dirname $0)/install_pecan.config ]; then
  . $(dirname $0)/install_pecan.config
fi


if [ -e /etc/redhat-release ]; then
  OS_VERSION="RH_$( sed -r 's/.* ([0-9]+)\..*/\1/' /etc/redhat-release )"
  HTTP_CONF="/etc/httpd/conf.d/"
  chmod o+x ${HOME}
else
  OS_VERSION="Ubuntu"
  HTTP_CONF="/etc/apache2/conf-available/"
fi

# actual install/update
echo "######################################################################"
echo "UPDATING MACHINE"
echo "######################################################################"
chmod 755 /home/carya/
case "$OS_VERSION" in
  RH_*)
    sudo yum update -y
    if [ "$SETUP_VM" != "" ]; then
      sudo sed -i -e "s/^127.0.0.1 .*\$/127.0.0.1 ${HOSTNAME}.pecan ${HOSTNAME} localhost localhost.localdomain localhost4 localhost4.localdomain4/" /etc/hosts
    fi
    ;;
  Ubuntu)
    sudo apt-get -qq -y update
    sudo apt-get -y dist-upgrade
    sudo apt-get -y purge --auto-remove
    if [ "$SETUP_VM" != "" ]; then
      sudo sed -i -e "s/^127.0.0.1[ \t].*\$/127.0.0.1\t${HOSTNAME}.vm ${HOSTNAME} localhost/" /etc/hosts
    fi
    ;;
  *)
    echo "Unknown OS"
    exit 1
    ;;
esac

echo "######################################################################"
echo "SETTING UP REPOS"
echo "######################################################################"
case "$OS_VERSION" in
  RH_5)
    sudo yum install -y wget
    sudo wget -O /etc/yum.repos.d/cornell.repo http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_CentOS-6/home:cornell_vrdc.repo
    sudo rpm -Uvh http://download.fedoraproject.org/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm
    ;;
  RH_6)
    sudo yum install -y wget
    sudo wget -O /etc/yum.repos.d/cornell.repo http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_CentOS-6/home:cornell_vrdc.repo
    sudo yum -y localinstall https://download.postgresql.org/pub/repos/yum/9.5/redhat/rhel-6-x86_64/pgdg-centos95-9.5-2.noarch.rpm
    sudo rpm -Uvh http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
    ;;
  RH_7)
    sudo yum install -y wget
    sudo wget -O /etc/yum.repos.d/cornell.repo wget http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_7/home:cornell_vrdc.repo
    sudo yum -y localinstall https://download.postgresql.org/pub/repos/yum/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-2.noarch.rpm
    sudo rpm -Uvh http://download.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-6.noarch.rpm
    setsebool -P httpd_can_network_connect 1
    ;;
  Ubuntu)
    if [ ! -e /etc/apt/sources.list.d/docker.list ]; then
      curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
      sudo sh -c 'echo "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs)   stable"  > /etc/apt/sources.list.d/docker.list'
    fi
    # if [ ! -e /etc/apt/sources.list.d/R.list ]; then
    #   sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -s -c`/" > /etc/apt/sources.list.d/R.list'
    #   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9
    # fi
    #if [ ! -e /etc/apt/sources.list.d/ruby.list ]; then
    #  sudo sh -c 'echo "deb http://ppa.launchpad.net/brightbox/ruby-ng/ubuntu trusty main" > /etc/apt/sources.list.d/ruby.list'
    #  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv C3173AA6
    #fi
    # if [ ! -e /etc/apt/sources.list.d/pgdg.list ]; then
    #   sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt `lsb_release -s -c`-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
    #   wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
    # fi
    sudo apt-get -qq -y update
    ;;
esac

echo "######################################################################"
echo "INSTALLING PACKAGES"
echo "######################################################################"
case "$OS_VERSION" in
  RH_*)
    sudo yum install -y git R gfortran openssl-devel
    sudo yum install -y openmpi openmpi-devel netcdf netcdf-openmpi netcdf-devel netcdf-openmpi-devel netcdf-fortran-devel netcdf-fortran-openmpi
    sudo ln -s /usr/lib64/openmpi/bin/mpicc /usr/bin/mpicc
    sudo ln -s /usr/lib64/openmpi/bin/mpif90 /usr/bin/mpif90
    # for ED
    sudo yum install -y hdf5-openmpi-devel
    # for LPJ-GUESS
    sudo yum install -y cmake
    # for DALEC
    sudo yum install -y gsl-devel liblas-devel lapack-devel
    # for PEcAn
    sudo yum install -y ed libpng-devel libpng12-devel libjpeg-turbo-devel jags4 jags4-devel python-devel udunits2-devel gdal-devel proj-devel proj-devel proj-nad proj-epsg libxml2-devel udunits2-devel gmp-devel
    # for PostgreSQL
    sudo yum install -y postgresql95-server postgresql95-devel postgis2_95
    # web gui
    sudo yum install -y httpd php php-pgsql php-xml expect expectk
    ;;
  Ubuntu)
    sudo apt-get -y install build-essential gfortran git r-base-core jags liblapack-dev libnetcdf-dev netcdf-bin bc libcurl4-gnutls-dev curl udunits-bin libudunits2-dev libgmp-dev python-dev libgdal-dev libproj-dev expect librdf0-dev
    sudo apt-get -y install openmpi-bin libopenmpi-dev
    sudo apt-get -y install libgsl0-dev libssl-dev
    # for maeswrap
    sudo apt-get -y install libx11-dev libgl1-mesa-dev libglu1-mesa-dev libfreetype6-dev
    # for R doc
    sudo apt-get -y install texinfo texlive-latex-base texlive-latex-extra texlive-fonts-recommended
    # BETY
    # sudo apt-get -y install ruby ruby-dev nodejs
    # for LPJ-GUESS
    sudo apt-get -y install cmake
    # for PostgreSQL
    # sudo apt-get -y install libdbd-pgsql postgresql-9.5 postgresql-client-9.5 libpq-dev postgresql-9.5-postgis-2.2 postgresql-9.5-postgis-scripts
    sudo apt-get -y install libdbd-pgsql postgresql-client libpq-dev
    # for web gui
    # sudo apt-get -y install apache2 libapache2-mod-php php libapache2-mod-passenger php-xml php-ssh2 php-pgsql
    sudo apt-get -y install apache2 libapache2-mod-php php php-xml php-ssh2 php-pgsql
    # Ubuntu 14.04 php5-pgsql libapache2-mod-php5 php5 and no php-xml
    sudo apt-get -y install docker-ce
    ;;
esac

echo "######################################################################"
echo "DOCKER"
echo "######################################################################"


sudo curl -L "https://github.com/docker/compose/releases/download/${DOCKER_COMPOSE}/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
sudo chmod 755 /usr/local/bin/docker-compose
sudo usermod -a -G docker carya

cd
mkdir -p postgres output portainer
chmod 777 postgres output portainer
cd output
if [ ! -e workflows ]; then
  ln -s workflows .
fi
cd

cat << EOF > docker-compose.yml
version: "3"

services:
  # Allow to see all docker containers running, restart and see log files.
  portainer:
    image: portainer/portainer:latest
    command:
      - --admin-password=\${PORTAINER_PASSWORD:-}
      - --host=unix:///var/run/docker.sock
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:9001:9000
    volumes:
      - /var/run/docker.sock:/var/run/docker.sock
      - portainer:/data

  # ----------------------------------------------------------------------
  # Access to the files generated and used by PEcAn, both through a
  # web interface (minio) as well using the thredds server.
  # ----------------------------------------------------------------------

  # webserver to handle access to data
  minio:
    image: minio/minio:latest
    command: server /data
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:9000:9000
    environment:
      - MINIO_ACCESS_KEY=\${MINIO_ACCESS_KEY:-carya}
      - MINIO_SECRET_KEY=\${MINIO_SECRET_KEY:-illinois}
    volumes:
      - pecan:/data

  # THREDDS data server
  thredds:
    image: pecan/thredds:\${PECAN_VERSION:-latest}
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:8080:8080
    volumes:
      - pecan:/data

  # ----------------------------------------------------------------------
  # Database to hold the data from PEcAn and BETY.
  # ----------------------------------------------------------------------

  postgres:
    image: mdillon/postgis:9.5
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:5432:5432
    volumes:
      - postgres:/var/lib/postgresql/data

  # ----------------------------------------------------------------------
  # BETY rails frontend to the database
  # ----------------------------------------------------------------------
  bety:
    image: pecan/bety:\${BETY_VERSION:-latest}
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:8000:8000
    environment:
      - UNICORN_WORKER_PROCESSES=1
      - SECRET_KEY_BASE=\${BETY_SECRET_KEY:-notasecret}
      - RAILS_RELATIVE_URL_ROOT=/bety
      - LOCAL_SERVER=\${BETY_LOCAL_SERVER:-99}
    depends_on:
      - postgres

  # ----------------------------------------------------------------------
  # PEcAn application
  # ----------------------------------------------------------------------

  # PEcAn documentation as well as PEcAn home page
  docs:
    image: pecan/docs:\${PECAN_VERSION:-latest}
    restart: unless-stopped
    networks:
      - pecan
    ports:
      - 127.0.0.1:8001:80

# ----------------------------------------------------------------------
# Name of network to be used by all containers
# ----------------------------------------------------------------------
networks:
  pecan:

# ----------------------------------------------------------------------
# Volumes used by the PEcAn stack. These volumes are used to make sure
# we have persistent data. You can use add the commented section to your
# docker-compose.override.yml to have the docker volumes placed at a
# specific location.
# ----------------------------------------------------------------------
volumes:
  postgres:
    driver_opts:
      type: none
      device: /home/carya/postgres
      o: bind
  pecan:
    driver_opts:
      type: none
      device: /home/carya/output
      o: bind
  portainer:
    driver_opts:
      type: none
      device: /home/carya/portainer
      o: bind
EOF

cat << EOF > start-containers.sh
#!/bin/bash

cd /home/carya
docker-compose pull
docker-compose -p carya up -d
EOF
chmod 755 start-containers.sh

# load postgres container
docker-compose pull
docker-compose -p carya up -d postgres
sleep 60
docker run --rm --network carya_pecan pecan/bety:latest initialize
docker-compose -p carya up -d

if [ ! -e ${HTTP_CONF}/docker.conf ]; then
  cat > /tmp/docker.conf << EOF
ProxyPass        /portainer/ http://localhost:9001/
ProxyPassReverse /portainer/ http://localhost:9001/
RedirectMatch permanent ^/portainer$ /portainer/

ProxyPass        /minio/ http://localhost:9000/minio/
ProxyPassReverse /minio/ http://localhost:9000/minio/
RedirectMatch permanent ^/minio$ /minio/

ProxyPass        /thredds/ http://localhost:8080/thredds/
ProxyPassReverse /thredds/ http://localhost:8080/thredds/
RedirectMatch permanent ^/thredds$ /thredds/

ProxyPass        /docs/ http://localhost:8001/docs/
ProxyPassReverse /docs/ http://localhost:8001/docs/
RedirectMatch permanent ^/docs$ /docs/
RedirectMatch permanent ^/$ /docs/

ProxyPass        /bety/ http://localhost:8000/bety/
ProxyPassReverse /bety/ http://localhost:8000/bety/
RedirectMatch permanent ^/bety$ /bety/
EOF
  sudo cp /tmp/docker.conf ${HTTP_CONF}/docker.conf
  rm /tmp/docker.conf
fi


echo "######################################################################"
echo "R"
echo "######################################################################"
if [ -z "${R_LIBS_USER}" ]; then
  echo 'export R_LIBS_USER=${HOME}/R/library' >> ${HOME}/.bashrc
  echo 'R_LIBS_USER=${HOME}/R/library' >> ${HOME}/.Renviron
  export export R_LIBS_USER=${HOME}/R/library
  mkdir -p ${R_LIBS_USER}

  echo "options(shiny.port = 6438)" >> ${HOME}/.Rprofile
  echo "options(shiny.launch.browser = 'FALSE')" >> ${HOME}/.Rprofile

  case "$OS_VERSION" in
    RH_*)
      echo 'export PATH=${PATH}:/usr/pgsql-9.5/bin' >> ${HOME}/.bashrc
      export PATH=${PATH}:/usr/pgsql-9.5/bin
      ;;
  esac
fi
echo 'if(!"devtools" %in% installed.packages()) install.packages("devtools")' | R --vanilla
echo 'if(!"udunits2" %in% installed.packages()) install.packages("udunits2", configure.args=c(udunits2="--with-udunits2-include=/usr/include/udunits2"))'  | R --vanilla

# packages for BrownDog shiny app
echo 'if(!"leaflet" %in% installed.packages()) install.packages("leaflet")' | R --vanilla
echo 'if(!"RJSONIO" %in% installed.packages()) install.packages("RJSONIO")' | R --vanilla

# packages for other shiny apps
echo 'if(!"DT" %in% installed.packages()) install.packages("DT")' | R --vanilla

#echo 'update.packages(ask=FALSE)' | sudo R --vanilla
echo 'x <- rownames(old.packages()); update.packages(ask=FALSE, oldPkgs=x[!x %in% "rgl"])' | sudo R --vanilla

#echo 'update.packages(ask=FALSE)' | R --vanilla
echo 'x <- rownames(old.packages()); update.packages(ask=FALSE, oldPkgs=x[!x %in% "rgl"])' | R --vanilla

echo "######################################################################"
echo "ED"
echo "######################################################################"
if [ ! -e ${HOME}/ED2 ]; then
  cd
  git clone https://github.com/EDmodel/ED2.git
  cd ${HOME}/ED2/ED/build
  curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
  if [ "$OS_VERSION" == "RH_6" ]; then
    sed -i 's/ -fno-whole-file//' make/include.mk.opt.VM
  fi
fi
cd ${HOME}/ED2
git pull
cd ED/build
./install.sh -g -p VM -c
./install.sh -g -p VM
sudo cp ed_2.1-opt /usr/local/bin/ed2.git
./install.sh -g -p VM -c

echo "######################################################################"
echo "SIPNET"
echo "######################################################################"
if [ ! -e ${HOME}/sipnet ]; then
  cd
  git clone https://github.com/PecanProject/sipnet.git
  sed -i 's#$(LD) $(LIBLINKS) \(.*\)#$(LD) \1 $(LIBLINKS)#' ${HOME}/sipnet/Makefile
fi

cd ${HOME}/sipnet/
git checkout r136
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.r136
make clean

cd ${HOME}/sipnet/
git checkout master
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.git
make clean

echo "######################################################################"
echo "MAESPA"
echo "######################################################################"
if [ ! -e ${HOME}/maespa ]; then
  cd
  git clone https://bitbucket.org/remkoduursma/maespa.git
  echo 'install.packages("Maeswrap")'  | R --vanilla
fi
cd ${HOME}/maespa
make clean
make
sudo cp maespa.out /usr/local/bin/maespa.git
make clean

echo "######################################################################"
echo "BioCro"
echo "######################################################################"
echo 'devtools::install_github("ebimodeling/biocro@0.951")' | R --vanilla

echo "######################################################################"
echo "Linkages"
echo "######################################################################"
echo 'devtools::install_github("araiho/linkages_package")' | R --vanilla

echo "######################################################################"
echo "Preles"
echo "######################################################################"
echo 'devtools::install_url("http://isda.ncsa.illinois.edu/~kooper/PEcAn/models/Rpreles_1.0.tar.gz")' | R --vanilla

echo "######################################################################"
echo "DALEC"
echo "######################################################################"
if [ ! -e ${HOME}/dalec_EnKF_pub ]; then
  cd
  curl -o dalec_EnKF_pub.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/dalec_EnKF_pub.tgz
  tar zxf dalec_EnKF_pub.tgz
  rm dalec_EnKF_pub.tgz
fi
cd ${HOME}/dalec_EnKF_pub
make clean
make dalec_EnKF
make dalec_seqMH
sudo cp dalec_EnKF dalec_seqMH /usr/local/bin
make clean

echo "######################################################################"
echo "GDAY"
echo "######################################################################"
if [ ! -e ${HOME}/GDAY ]; then
  cd
  git clone https://github.com/mdekauwe/GDAY.git
fi
cd ${HOME}/GDAY
git pull
cd src
make
sudo cp gday /usr/local/bin
make clean

echo "######################################################################"
echo "PECAN"
echo "######################################################################"

echo 'if(!"rgl" %in% installed.packages()) install.packages("rgl")' | R --vanilla

if [ ! -e ${HOME}/pecan ]; then
  cd
  git clone https://github.com/PecanProject/pecan.git
fi
cd ${HOME}/pecan
git pull
if [ "${PECAN_BRANCH}" != "" ]; then
  git checkout ${PECAN_BRANCH}
fi
make

if [ ! -e ${HOME}/pecan/web/config.php ]; then
  sed -e "s#browndog_url=.*#browndog_url=\"${BROWNDOG_URL}\";#" \
      -e "s#browndog_username=.*#browndog_username=\"${BROWNDOG_USERNAME}\";#" \
      -e "s#browndog_password=.*#browndog_password=\"${BROWNDOG_PASSWORD}\";#" \
      -e "s/carya/$USER/g" ${HOME}/pecan/web/config.example.php > ${HOME}/pecan/web/config.php
fi

if [ ! -e ${HTTP_CONF}/pecan.conf ]; then
  cat > /tmp/pecan.conf << EOF
Alias /pecan ${HOME}/pecan/web
<Directory ${HOME}/pecan/web>
  DirectoryIndex index.php
  Options +ExecCGI
  Require all granted
</Directory>
EOF
  sudo cp /tmp/pecan.conf ${HTTP_CONF}/pecan.conf
  rm /tmp/pecan.conf
fi

echo "######################################################################"
echo "DATA"
echo "######################################################################"
cd ${HOME}

if [ ! -e ${HOME}/sites ]; then
  curl -s -o sites.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/sites.tgz
  tar zxf sites.tgz
  sed -i -e "s#/home/kooper/Projects/EBI#${HOME}#" sites/*/ED_MET_DRIVER_HEADER
  rm sites.tgz
fi

if [ ! -e ${HOME}/inputs ]; then
  curl -s -o inputs.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/inputs.tgz
  tar zxf inputs.tgz
  rm inputs.tgz
fi

if [ ! -e ${HOME}/lpj-guess/cru_1901_2006.bin ]; then
  if [ ! -d ${HOME}/lpj-guess ]; then
    mkdir ${HOME}/lpj-guess
  fi
  curl -s -o ${HOME}/lpj-guess/cru_1901_2006.bin http://isda.ncsa.illinois.edu/~kooper/PEcAn/data/cru_1901_2006.bin
fi

if [ ! -e ${HOME}/plot ]; then
  curl -s -o plot.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/plot.tgz
  tar zxf plot.tgz
  rm plot.tgz
fi

if [ ! -e ${HOME}/sites/Santarem_Km83 ]; then
  curl -s -o Santarem_Km83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/Santarem_Km83.zip
  unzip -q -d sites Santarem_Km83.zip
  sed -i -e "s#/home/pecan#${HOME}#" sites/Santarem_Km83/ED_MET_DRIVER_HEADER
  rm Santarem_Km83.zip
fi

if [ ! -e ${HOME}/testrun.s83 ]; then
  curl -s -o testrun.s83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.s83.zip
  unzip -q testrun.s83.zip
  sed -i -e "s#/home/pecan#${HOME}#" testrun.s83/ED2IN
  rm testrun.s83.zip
fi

if [ ! -e ${HOME}/ed2ws.harvard ]; then
  curl -s -o ed2ws.harvard.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ed2ws.harvard.tgz
  tar zxf ed2ws.harvard.tgz
  mkdir ed2ws.harvard/analy ed2ws.harvard/histo
  sed -i -e "s#/home/pecan#${HOME}#g" ed2ws.harvard/input_harvard/met_driver/HF_MET_HEADER ed2ws.harvard/ED2IN ed2ws.harvard/*.r
  rm ed2ws.harvard.tgz
fi

if [ ! -e ${HOME}/testrun.PDG ]; then
  curl -s -o testrun.PDG.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.PDG.zip
  unzip -q testrun.PDG.zip
  sed -i -e "s#/home/pecan#${HOME}#" testrun.PDG/Met/PDG_MET_DRIVER testrun.PDG/Template/ED2IN
  sed -i -e 's#/n/scratch2/moorcroft_lab/kzhang/PDG/WFire_Pecan/##' testrun.PDG/Template/ED2IN
  rm testrun.PDG.zip
fi

if [ ! -e ${HOME}/create_met_driver ]; then
  curl -s -o create_met_driver.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/create_met_driver.tar.gz
  tar zxf create_met_driver.tar.gz
  rm create_met_driver.tar.gz
fi

${HOME}/pecan/scripts/add.models.sh
${HOME}/pecan/scripts/add.data.sh

echo "######################################################################"
echo "RSTUDIO SERVER"
echo "######################################################################"
if [ "${RSTUDIO_SERVER}" != "" ]; then
  case "$OS_VERSION" in
    RH_*)
      curl -s -o rstudio.rpm https://download2.rstudio.org/rstudio-server-rhel-${RSTUDIO_SERVER}-x86_64.rpm
      sudo yum -y install --nogpgcheck rstudio.rpm
      rm rstudio.rpm
      ;;
    Ubuntu)
      sudo apt-get -y install gdebi-core
      if [ $( uname -m ) == "x86_64" ]; then
        curl -s -o rstudio.deb https://download2.rstudio.org/rstudio-server-${RSTUDIO_SERVER}-amd64.deb
      elif [ $( uname -m ) == "i686" ]; then
        curl -s -o rstudio.deb https://download2.rstudio.org/rstudio-server-${RSTUDIO_SERVER}-i386.deb
      fi
      sudo gdebi -q -n rstudio.deb
      rm rstudio.deb
      ;;
  esac

  if [ ! -e ${HTTP_CONF}/rstudio.conf  ]; then
    sudo sh -c 'echo "www-address=127.0.0.1" >> /etc/rstudio/rserver.conf'
    sudo sh -c 'echo "r-libs-user=~/R/library" >> /etc/rstudio/rsession.conf'

    cat > /tmp/rstudio.conf << EOF
ProxyPass        /rstudio/ http://localhost:8787/
ProxyPassReverse /rstudio/ http://localhost:8787/
RedirectMatch permanent ^/rstudio$ /rstudio/
EOF
    sudo cp /tmp/rstudio.conf ${HTTP_CONF}/rstudio.conf
    rm /tmp/rstudio.conf
  fi
fi

echo "######################################################################"
echo "SHINY SERVER"
echo "######################################################################"
if [ "${SHINY_SERVER}" != "" -a $( uname -m ) == "x86_64" ]; then
  sudo su - -c "R -e \"install.packages(c('rmarkdown', 'shiny'))\""

  R -e "install.packages(c('https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.28.0.tar.gz', 'http://www.bioconductor.org/packages/release/bioc/src/contrib/graph_1.60.0.tar.gz'), repos=NULL)"
  R -e "devtools::install_github('duncantl/CodeDepends')"
  #R -e "devtools::install_github('OakleyJ/SHELF')"
  R -e "install.packages(c('shinythemes', 'shinytoastr', 'plotly'))"

  cd 

  case "$OS_VERSION" in
    RH_*)
      curl -s -o shiny.rpm https://download3.rstudio.org/centos5.9/x86_64/shiny-server-${SHINY_SERVER}-rh5-x86_64.rpm
      sudo yum -y install --nogpgcheck shiny.rpm
      rm shiny.rpm
      ;;
    Ubuntu)
      sudo apt-get -y install gdebi-core
      curl -s -o shiny.deb https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-${SHINY_SERVER}-amd64.deb
      sudo gdebi -q -n shiny.deb
      rm shiny.deb
      ;;
  esac

  if [ ! -e ${HTTP_CONF}/shiny.conf ]; then
    cat > /tmp/shiny-server.conf << EOF
run_as shiny;
server {
  listen 3838;
  location / {
    run_as ${USER};
    site_dir ${HOME}/pecan/shiny;
    log_dir /var/log/shiny-server;
    directory_index on;
  }
}
EOF
    sudo cp /tmp/shiny-server.conf /etc/shiny-server/shiny-server.conf
    rm /tmp/shiny-server.conf

    cat > /tmp/shiny.conf << EOF
ProxyPass        /shiny/ http://localhost:3838/
ProxyPassReverse /shiny/ http://localhost:3838/
RedirectMatch permanent ^/shiny$ /shiny/
EOF
    sudo cp /tmp/shiny.conf ${HTTP_CONF}/shiny.conf
    rm /tmp/shiny.conf
  fi
fi

echo "######################################################################"
echo "RESTART SERVICES"
echo "######################################################################"
case "$OS_VERSION" in
  RH_6)
    cat > /tmp/iptables << EOF
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [3:556]
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p icmp -j ACCEPT
-A INPUT -i lo -j ACCEPT
-A INPUT -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 443 -j ACCEPT
-A INPUT -j REJECT --reject-with icmp-host-prohibited
-A FORWARD -j REJECT --reject-with icmp-host-prohibited
COMMIT
EOF
    cp /tmp/iptables /etc/sysconfig/iptables
    rm /tmp/iptables
    /sbin/service iptables reload

    if [ ! -e /etc/init.d/rstudio-server -a -e /usr/lib/rstudio-server/extras/init.d/redhat/rstudio-server ]; then
      sudo cp /usr/lib/rstudio-server/extras/init.d/redhat/rstudio-server /etc/init.d
      sudo chkconfig rstudio-server on
    fi
    sudo service rstudio-server restart
    if [ ! -e /etc/init.d/shiny-server -a -e /opt/shiny-server/config/init.d/redhat/shiny-server ]; then
      sudo cp /opt/shiny-server/config/init.d/redhat/shiny-server /etc/init.d
      sudo chkconfig shiny-server on
    fi
    sudo service shiny-server restart
    sudo service httpd restart
    ;;
  RH_7)
    sudo systemctl restart rstudio-server.service
    sudo systemctl restart shiny-server.service
    sudo systemctl restart httpd.service
    ;;
  Ubuntu)
    sudo a2enmod proxy_http
    sudo a2enconf docker pecan
    if [ -e ${HTTP_CONF}/rstudio.conf ]; then
      sudo a2enconf rstudio
      sudo service rstudio-server restart
    fi
    if [ -e ${HTTP_CONF}/shiny.conf ]; then
      sudo a2enconf shiny
      sudo service shiny-server restart
    fi
    sudo service apache2 restart
    ;;
esac

echo "######################################################################"
echo "PalEON"
echo "######################################################################"
if [ "$SETUP_PALEON" != "" ]; then
  echo 'if(!"neotoma" %in% installed.packages()) install.packages("neotoma")' | R --vanilla
  echo 'if(!"R2jags" %in% installed.packages()) install.packages("R2jags")' | R --vanilla

  if [ ! -e ${HOME}/Camp2016 ]; then
    cd
    git clone https://github.com/PalEON-Project/Camp2016.git
  fi
  cd ${HOME}/Camp2016
  git pull
  R --vanilla < testInstall.R

  if [ ! -e ${HOME}/LinBacon_2.2 ]; then
    cd
    curl -o LinBacon_2.2.zip http://chrono.qub.ac.uk/blaauw/LinBacon_2.2.zip
    unzip LinBacon_2.2.zip
    rm LinBacon_2.2.zip
  fi
  cd ${HOME}/LinBacon_2.2/cpp
  rm -f *.o
  make -f makefileLinux
  rm *.o

  if [ ! -e ${HOME}/clam ]; then
    cd
    curl -o clam.zip http://chrono.qub.ac.uk/blaauw/clam.zip
    unzip clam.zip
    rm clam.zip
  fi
fi

echo "######################################################################"
echo "SETUP_VM"
echo "######################################################################"
if [ "${SETUP_VM}" != "" ]; then
  # extra packages
  case "$OS_VERSION" in
    RH_*)
      sudo yum -y install hdf5-tools cdo nco netcdf-bin ncview gdb emacs ess nedit
      ;;
    Ubuntu)
      sudo apt-get -y install hdf5-tools cdo nco netcdf-bin ncview gdb emacs ess nedit
      ;;
  esac

  # MOTD
  VERSION=$( awk '/Version: / { print $2 }' $HOME/pecan/base/all/DESCRIPTION )
  cat > /tmp/motd << EOF
PEcAn version ${VERSION}

For more information about:
Pecan    - http://pecanproject.org
BETY     - http://www.betydb.org

For a list of all models currently supported see:
https://pecan.gitbooks.io/pecan-documentation/content/models/
EOF
  sudo cp /tmp/motd /etc/motd
  rm /tmp/motd

  # fix prompt
  sudo sed -i 's/\\h/\\H/g' /etc/bash.bashrc
  sudo sed -i 's/\\h/\\H/g' /etc/profile
  sed -i 's/\\h/\\H/g' ${HOME}/.bashrc
fi