Create default StudyInfo.csv

workflow/qhtcp-workflow

@@ -411,19 +411,36 @@ init_project() {
 
   [[ -d $PROJECT_SCANS_DIR ]] || (mkdir -p "$PROJECT_SCANS_DIR" || return 1)
 
+
+  # Create the study info file
+  if [[ ! -f $STUDY_INFO_FILE ]]; then
+    echo "Create a default study info file?";
+    if ask "You can edit this file in the qhtcp module"; then
+      cat <<-EOF > "$STUDY_INFO_FILE"
+				"ExpNumb","ExpLabel","BackgroundSD","ZscoreJoinSD","AnalysisBy"
+			EOF
+    fi
+  fi
+
+
   # Write skeleton files in csv
   # If we have to convert to xlsx later, so be it
-  cat <<-EOF > "$DRUG_MEDIA_FILE"
+  echo "In the future we will copy the DrugMedia file from robot here"
+  # cat <<-EOF > "$DRUG_MEDIA_FILE"
 		
 		
 		
-	EOF
+	# EOF
   
-  cat <<-EOF > "$MASTER_PLATE_FILE"
+
+  # TODO here we'll copy scans from robot but for now let's pause and wait for transfer
+  echo "In the future we will copy the MasterPlate file from robot here"
+
+  # cat <<-EOF > "$MASTER_PLATE_FILE"
 	
 	
 	
-	EOF
+	# EOF
 
   # TODO here we'll copy scans from robot but for now let's pause and wait for transfer
   echo "In the future we will copy scans from robot here"
@@ -611,7 +628,7 @@ easy() {
     done
 
     # Copy templates
-    rsync -a "$EASY_DIR"/{figs,Ptmats} "$EASY_RESULTS_DIR"
+    rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
 
     # Launch matlab
     # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
@@ -706,8 +723,6 @@ module qhtcp
 qhtcp() {
   debug "Running: ${FUNCNAME[0]}"
 
-
-  
   if [[ -d $QHTCP_PROJECT_DIR ]]; then
     echo "A project already exists at $QHTCP_PROJECT_DIR"
     ask "Safely update $QHTCP_PROJECT_DIR from the $QHTCP_TEMPLATE_DIR template?"
@@ -749,7 +764,7 @@ qhtcp() {
   # Ask user to edit STUDY_INFO_FILE
   if ! ((YES)) && ask "Would you like to edit $STUDY_INFO_FILE to add or modify studies?"; then
     cat <<-EOF 
-			Give each experiment the labels you wish to be used for the plots and specific files. 
+			Give each experiment labels to be used for the plots and specific files. 
 			Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
 
 			Auto-entry suggestion: $next_study_entry