From 7cc02641779f3105ec4c0b83f7dfbda8b729fb18 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Fri, 2 Aug 2024 20:09:11 -0400
Subject: [PATCH] Fix R lib install

---
 workflow/qhtcp-workflow | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 3ef8b8e9..a246f739 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -275,7 +275,7 @@ backup() {
 }
 
 # @description Prints a helpful message add program start
-print_header() {
+interactive_header() {
   debug "Running: ${FUNCNAME[0]}"
 
   cat <<-'EOF'
@@ -1643,18 +1643,6 @@ main() {
   declare -g RSCRIPT="${RSCRIPT:-$(which Rscript 2>/dev/null)}"
   declare -g MATLAB="${MATLAB:-$(which matlab 2>/dev/null)}"
 
-  # Use a custom R library
-  if [[ -z $R_LIBS_USER || $R_LIBS_USER != "$HOME/R/$SCRIPT_NAME" ]]; then
-    echo "This script uses a custom R library at $HOME/R/$SCRIPT_NAME"
-    echo "You can install the R dependencies to this library using the install_dependencies module"
-    if ((YES)) || ask "Would you like to make this library the default for your user?"; then
-      echo "Adding R_LIBS_USER=$HOME/R/$SCRIPT_NAME to your .bashrc"
-      echo "export R_LIBS_USER=$HOME/R/$SCRIPT_NAME" >> "$HOME/.bashrc"
-    fi
-  else
-    debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME"
-  fi
-
   # Global vars
   SCRIPT_NAME="${BASH_SOURCE[0]}"
   SCRIPT=$(realpath -s "${BASH_SOURCE[0]}")
@@ -1714,6 +1702,19 @@ main() {
     fi
   fi
 
+  # Ask to make our custom R library the default
+  if [[ -z $R_LIBS_USER || $R_LIBS_USER != "$HOME/R/$SCRIPT_NAME" ]]; then
+    echo "This script uses a custom R library at $HOME/R/$SCRIPT_NAME"
+    echo "You can install the R dependencies to this library using the install_dependencies module"
+    if ((YES)) || ask "Would you like to make this library the default for your user?"; then
+      echo "Adding R_LIBS_USER=$HOME/R/$SCRIPT_NAME to your .bashrc"
+      echo "export R_LIBS_USER=$HOME/R/$SCRIPT_NAME" >> "$HOME/.bashrc"
+    fi
+  else
+    debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME"
+  fi
+
+
   # Make sure we are using the absolute path
   OUT_DIR=$(realpath -s "$OUT_DIR")
 
@@ -1725,7 +1726,7 @@ main() {
 
   parse_input "$@" # parse arguments with getopt
 
-  print_header "$@"
+  interactive_header "$@"
 
   # # Prompt user for the PROJECT if we still don't have one
   # if [[ ${#PROJECTS[@]} -eq 0 ]]; then