R-3.6.3_Bioconductor_package_install

#!/usr/bin/env bash

###############################################
# Installing a single R additional package
#
# by Brian Alston, November 2016 V1.0 
#
# Updated June 2017 for R 3.4.0 / Bioconductor 3.5
# Updated May 2020 for R 3.6.3 and Bioconductor 3.10
#
# usage: R-Bioconductor_package_install <R package name>
#
# Will need modules: r/r-3.6.3_bc-3.10

set -e

VERSION=${VERSION:-3.6.3}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/R/R-${VERSION}-OpenBLAS}
export RLIB_MAIN=${RLIB_MAIN:-${INSTALL_PREFIX}/lib64/R/library}
export RLIB_DB=${RLIB_DB:-/home/ccspapp/Scratch/R/R-${VERSION}-OpenBLAS/library}
export REPROS=${REPROS:-https://cloud.r-project.org/}
LOCALDIR=${LOCALDIR:-/shared/ucl/apps/build_scripts/files/R_UCL}

export PATH=$INSTALL_PREFIX/bin:$PATH

dirname=$(dirname $0 2>/dev/null || pwd)
INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
source ${INCLUDES_DIR}/module_maker_inc.sh
source ${INCLUDES_DIR}/require_inc.sh

# require r/recommended
# require r/new
require r/r-3.6.3_bc-3.10

if [ $# -ne 1 ]; then
	echo "usage: R-package_install <R package name>"
	exit 1
fi
PACKAGE=$1

temp_dir=`mktemp -d -p /dev/shm`
# temp_dir='/home/ccspapp/Software/R'
echo "Building in $temp_dir ..."
cd $temp_dir
module list
read -p "Press [Enter] key to start ..."

cat > R_script <<EOF
mainLib <- Sys.getenv ("RLIB_MAIN");
dbLib <- Sys.getenv ("RLIB_DB");
repros <- Sys.getenv ("REPROS");
mainLib;
dbLib;
repros;

# Download the Bioconductor installer and install the base package

if (!requireNamespace ("BiocManager"))
    install.packages ("BiocManager", repos=repros)
BiocManager::install ()

# Install Bioconductor package

BiocManager::install ("$PACKAGE", type="source", lib=mainLib);

EOF

echo "Installing $PACKAGE and dependencies ..."
R --no-save < R_script
echo "Done."