aq-inst-cran.in

#!/bin/sh

if [ "x$(which apt-get)" != x ]
then
	read -p "You seem to have a Debianish system. Do you want me to use cran2deb? (Choose no if you have used QIIME's app-deploy script to install QIIME) [y/n] " USECRAN
	if [ "$USECRAN" = y -o "$USECRAN" = Y ]
	then
		if ! grep "http://debian.cran.r-project.org/rep" /etc/apt/sources.list /etc/apt/sources.list.d/*.list
		then
			echo "deb http://debian.cran.r-project.org/rep cran2deb main" > /etc/apt/source.list.d/cran2deb.list && \
			wget -O- http://debian.cran.r-project.org/key.asc | apt-key add - && \
			apt-get update || echo "Failed to add cran2deb." && exit 1
		fi
		for each in @R_PKGS@
		do
			apt-get install r-cran-${each}
		done
		exit 0
	fi
fi

for each in @R_PKGS@
do
	echo "install.packages(\"${each}\");" | R --no-save -q
done