Use a custom local R library

workflow/qhtcp-workflow

@@ -66,7 +66,7 @@ shopt -s extglob
 JAVA="${JAVA:-java}"
 PYTHON="${PYTHON:-python3}"
 PERL="${PERL:-perl}"
-RSCRIPT="${RSCRIPT:-Rscript}"
+RSCRIPT="${RSCRIPT:-"R_LIBS_USER=~/R/qhtcp-workflow Rscript=Rscript"}"
 
 # @section Help
 # @description Print a helpful message
@@ -467,8 +467,9 @@ install_dependencies() {
 
   # Install perl CPAN modules
   echo "Installing perl CPAN modules"
+  echo "It is recommended to use the local::lib perl library if prompted"
   debug "cpan -I ${depends_perl[*]}"
-  cpan -I "${depends_perl[@]}"
+  cpan -I -i "${depends_perl[@]}"
 
   # Install R packages
   echo "Installing R packages"
@@ -485,6 +486,8 @@ install_dependencies() {
   debug "$RSCRIPT -e install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
   "$RSCRIPT" -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
   "$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")"
+
+  hash matlab &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
 }