Script to install local versions of R libraries needed by CRAFT-GP pipeline

install_craft_gp_R_libs.sh

#!/usr/bin/bash
#
packages="dplyr coloc readr tidyr stringr optparse"

export INSTALL_DIR=$(pwd)/R_LIBS/CRAFT-GP
if [ ! -d $INSTALL_DIR ] ; then
    mkdir -p $INSTALL_DIR
fi
export R_LIBS=$R_LIBS:$INSTALL_DIR
for package in $packages ; do
   package_info=$(echo 'installed.packages()[,c("Package","Version")]' | R --vanilla | grep ^$package)
   echo $package: $package_info
   if [ ! -z "$package_info" ] ; then
      echo "FOUND $package: $package_info"
   else
      R --vanilla <<EOF
install.packages("$package",lib="$INSTALL_DIR",repos="http://cran.ma.imperial.ac.uk/")
q()
EOF
   fi
done

After running the script you'll need to add the dependencies to the R_LIBS environment variable e.g.

export R_LIBS=$(pwd)/R_LIBS/CRAFT-GP