install-ancestry-stack.sh

#! /bin/bash

# check to make sure script is running as root
if [ "$EUID" -ne 0 ]
  then echo "Please run this script using sudo to make sure all packages install correctly."
  exit
fi

# attempt to disable user interaction/pauses during installation
export DEBIAN_FRONTEND=noninteractive

# update packages repo and install unzip to be sure its there
apt --assume-yes update
apt --assume-yes install unzip

# install the latest stable version of R and Rscript
# taken from (https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04)
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'

# update again
apt --assume-yes update

# install r-base
apt --assume-yes install r-base

# install ggplot2 (version 3.1.0)
GGPLOT2_FILENAME="ggplot2_3.1.0.tar.gz"
wget https://cran.r-project.org/src/contrib/$GGPLOT2_FILENAME
R CMD INSTALL $GGPLOT2_FILENAME

# install plink (beta 6.7 stable)
PLINK_FILENAME="plink_linux_x86_64_20181202.zip"
wget http://s3.amazonaws.com/plink1-assets/$PLINK_FILENAME
mkdir plink_install
unzip $PLINK_FILENAME -d plink_install
mv plink_install/* /usr/local/bin

# install admixture
# taken from (http://hpc.ilri.cgiar.org/admixture-software)
wget http://software.genetics.ucla.edu/admixture/binaries/admixture_linux-1.3.0.tar.gz
tar -xvf admixture_linux-1.3.0.tar.gz
cd admixture_linux-1.3.0/
cp -r . /usr/local/bin

cd ..

# cleanup
echo "Cleaning up..."
rm -r admixture_linux-1.3.0
rm -r plink_install
rm $PLINK_FILENAME
rm $GGPLOT2_FILENAME
rm admixture_linux-1.3.0.tar.gz

echo "Everything installed successfully."