Refactor some env vars

workflow/qhtcp-workflow

@@ -569,6 +569,7 @@ easy() {
 		'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder. 
 	EOF
 
+  EASY_DIR="$APPS_DIR/matlab/easy"
   script="$EASY_DIR/EASYConsole.m"
 
   # Copy templates
@@ -703,7 +704,8 @@ qhtcp() {
   OUT_DIR="/mnt/data/out/qhtcp"
   STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
   QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
-  APPS_DIR="$QHTCP_PROJECT_DIR/apps"
+  QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
+  STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
   STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
   
   if [[ -d $QHTCP_PROJECT_DIR ]]; then
@@ -781,7 +783,7 @@ qhtcp() {
   # TODO eventually we could run this on multiple results dirs simultaneously with some refactoring
   if ((YES)) || [[ ${#EASY_RESULTS_DIRS[@]} -eq 1 ]]; then
     # In automatic mode just choose the first OUT DIR in the list
-    EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose
+    EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose the frist one
   else
     echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR"
     echo "Here is a list: "
@@ -1468,9 +1470,7 @@ main() {
 
   # Global directory variables
   TEMPLATES_DIR="$SCRIPT_DIR/templates"
-  QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
-  STUDY_TEMPLATE_DIR="$QHTCP_TEMPLATE_DIR/ExpTemplate"
-  EASY_DIR="$SCRIPT_DIR/apps/matlab/easy"
+  APPS_DIR="$SCRIPT_DIR/apps"
   DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
   SCANS="${SCANS:-"./scans":-"/mnt/data/ExpJobs"}"
   SCANS_HEIRARCHY=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs") # search for an existing scans dir in this order