atlantisvm_Ubuntu20

#!/bin/bash

echo "This script expects Ubuntu Server 20.04.2 LTS (Focal Fossa)"
echo "Will install all dependencies, libraries, Rstudio and needed packages to run Atlantis and analyze output"

sudo timedatectl set-timezone America/Los_Angeles

sudo apt-get update -y
sudo apt-get dist-upgrade -y

sudo apt-get -y --no-install-recommends install \
    autoconf \
    automake \
    build-essential \
    libcurl4 \
    libcurl4-openssl-dev \
    curl \
    cargo \
    gdal-bin \
    flip \
    libcairo2 \
    libavfilter-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libcairo-5c0 \
    libapparmor1 \
    libhdf5-dev \
    libnetcdf-dev \
    libudunits2-dev \
    libxml2-dev \
    libssl-dev \
    libv4l-0 \
    libgeotiff5 \
    libglu1-mesa-dev \
    libpoppler-cpp-dev \
    libprotobuf-dev \
    librsvg2-dev \
    libx11-dev \
    lsscsi \
    openjdk-8-jdk \
    python2 \
    proj-data \
    protobuf-compiler \
    htop \
    openssl \
    rpm \
    mesa-common-dev \
    netcdf-bin \
    ntp \
    ntpdate \
    texlive-latex-extra \
    nco \
    cdo \
    unzip \
    gfortran
 
#use this to install Proj4 which is required for Atlantis 
#https://gist.github.com/robinkraft/2a8ee4dd7e9ee9126030
#http://grasswiki.osgeo.org/wiki/Compile_and_Install_Ubuntu#PROJ4
#uninstall   proj-bin libproj-dev if present
#look for proj with locate libproj.so
# sudo apt install mlocate

 
sudo apt-get install -y subversion make

cd /tmp
svn co http://svn.osgeo.org/metacrs/proj/branches/4.8/proj/ --non-interactive --trust-server-cert-failures unknown-ca,cn-mismatch,expired,not-yet-valid,other
cd /tmp/proj/nad
sudo wget http://download.osgeo.org/proj/proj-datumgrid-1.5.zip

unzip -o -q proj-datumgrid-1.5.zip

#make distclean

cd /tmp/proj/

./configure  &&  make  &&  sudo make install && sudo ldconfig 
 
#these might be needed to install spatial R programs but can conflict with Atlantis proj4

#https://github.com/r-spatial/sf#multiple-gdal-geos-andor-proj-versions-on-your-system
#https://stackoverflow.com/questions/60759865/error-when-installing-sf-in-r-double-free-or-corruption
#to remove a respository https://askubuntu.com/questions/866901/what-can-i-do-if-a-repository-ppa-does-not-have-a-release-file
#sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
#sudo apt-get update -y
#sudo apt-get upgrade -y
#sudo apt-get dist-upgrade -y
#sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev -y
  
#sudo add-apt-repository -y ppa:opencpu/jq
#sudo apt-get update -qq
#sudo apt-get install libjq-dev -y

sudo apt-get -f install -y # missing dependencies
sudo apt autoremove -y #unused packages

echo "Install R"
#http://cran.rstudio.com/bin/linux/ubuntu/
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
sudo apt install --no-install-recommends r-base -y
sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ -y

echo "Install R studio" 

sudo apt-get install gdebi-core -y
wget https://download2.rstudio.org/server/focal/amd64/rstudio-server-2023.12.1-402-amd64.deb
sudo gdebi --n rstudio-server-2023.12.1-402-amd64.deb
echo "Install AzCopy" 

#to uninstall azcopy use https://github.com/MicrosoftDocs/azure-docs/issues/18771
wget -O azcopy_linux_amd64_10.20.1.tar https://aka.ms/downloadazcopy-v10-linux
tar -xzf azcopy_linux_amd64_10.20.1.tar
sudo cp ./azcopy_linux_amd64_*/azcopy /usr/bin/

echo "Install AzCLI"

curl -sL https://aka.ms/InstallAzureCLIDeb | sudo bash
sudo apt-get update
sudo apt-get install ca-certificates curl apt-transport-https lsb-release gnupg

sudo mkdir -p /etc/apt/keyrings
curl -sLS https://packages.microsoft.com/keys/microsoft.asc |
    gpg --dearmor |
    sudo tee /etc/apt/keyrings/microsoft.gpg > /dev/null
sudo chmod go+r /etc/apt/keyrings/microsoft.gpg

AZ_REPO=$(lsb_release -cs)
echo "deb [arch=`dpkg --print-architecture` signed-by=/etc/apt/keyrings/microsoft.gpg] https://packages.microsoft.com/repos/azure-cli/ $AZ_REPO main" |
    sudo tee /etc/apt/sources.list.d/azure-cli.list
    
sudo apt-get update
if [ -d $HOME/bin ]; then
PATH=$PATH:$HOME/bin
fi