From b77f45969225a037e954eb15ab4ddc7ff8b7e094 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Sun, 4 Aug 2024 21:38:33 -0400
Subject: [PATCH] Move R path to install_dependencies

---
 workflow/qhtcp-workflow | 42 ++++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 22 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 9c5ca503..58bd3eba 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -508,24 +508,6 @@ interactive_header() {
   fi
   echo ""
 
-  # 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 local 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 R library the default for your user?"; then
-      line="export R_LIBS_USER=$HOME/R/$SCRIPT_NAME"
-      if ! grep -qF "$line" ~/.bashrc; then
-        echo "Adding $line to your .bashrc"
-        echo "If you use a different shell, update your R_LIBS_USER environment variable accordingly"
-        echo "$line" >> ~/.bashrc
-      fi
-    fi
-    declare -gx R_LIBS_USER="$HOME/R/$SCRIPT_NAME"
-  else
-    debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME"
-  fi
-  echo ""
-
   # Let user choose or add project(s)
   if [[ ${#PROJECTS[@]} -eq 0 ]]; then
     num=$((${#projects[@]}))
@@ -533,11 +515,10 @@ interactive_header() {
       ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
     else
       for ((c=1; c<2; c++)); do # safe loop that only runs once
-        echo 
         cat <<-EOF
-					Enter project number(s) to analyze:
-					  * <Enter> for the latest project ($num) (default)
-					  * A comma-separated list of project numbers (2,5,12)
+					${underline}Enter project number(s) to analyze${nounderline}
+					  * <Enter> for the latest project (default)
+					  * A comma-separated list of project numbers: 2,5,12
 					  * 0 to add a new project
 				EOF
         ((YES)) || read -r -p "($num): " response
@@ -730,6 +711,23 @@ install_dependencies() {
     "$RSCRIPT" -e "BiocManager::install(\"$d\", lib=\"$R_LIBS_USER\")"
   done
 
+  # Ask to make our custom R library the default
+  if [[ $R_LIBS_USER == "$HOME/R/$SCRIPT_NAME" ]]; then
+    line="export R_LIBS_USER=$R_LIBS_USER"
+    if ! grep -qF "$line" "$HOME/.bashrc"; then
+      echo "This script uses a local R library at $HOME/R/$SCRIPT_NAME"
+      echo "You can install the R dependencies to this library using the install_dependencies module"
+    fi
+    if ((YES)) || ask "Would you like to make this R library the default for your user?"; then
+      echo "Adding $line to your .bashrc"
+      echo "If you use a different shell, update your R_LIBS_USER environment variable accordingly"
+      echo "$line" >> ~/.bashrc
+    fi
+  else
+    debug "R_LIBS_USER is set to a custom path"
+  fi
+  echo ""
+
   hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
 }