Add a safe main loop

workflow/qhtcp-workflow

@@ -427,7 +427,7 @@ install_dependencies() {
 
   # Dependency arrays
   depends_rpm=(graphviz pandoc pdftk-java gd-devel perl-CPAN shdoc nano rsync coreutils libcurl-devel openssl-devel)
-  depends_deb=(graphviz pandoc pdftk-java libgd-dev perl shdoc nano rsync coreutils)
+  depends_deb=(graphviz pandoc pdftk-java libgd-dev perl shdoc nano rsync coreutils libcurl-dev openssl-dev)
   depends_brew=(graphiz pandoc gd pdftk-java shdoc nano perl rsync coreutils)
   depends_perl=(File::Map ExtUtils::PkgConfig GD GO::TermFinder)
   depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 
@@ -1644,8 +1644,16 @@ main() {
   declare -g MATLAB="${MATLAB:-$(which matlab 2>/dev/null)}"
 
   # Use a custom R library
-  declare -gx R_LIBS_USER="$HOME/R/$SCRIPT_NAME"
-  [[ -d "$R_LIBS_USER" ]] || mkdir -p "$R_LIBS_USER"
+  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="${BASH_SOURCE[0]}"
@@ -1795,9 +1803,14 @@ main() {
         "${SUBMODULES[i]}" "${cmds[@]}"
       continue 2 # skip the command string
     done
+
+
   done
 }
 
-main "$@"
+# (Safe) main loop
+for ((i=0; i<=1; i++)); do
+  main "$@" && i=0 # on successful run, reset the counter
+done
 
 exit $?