From 5a4bb8c90acc1fe2b90beb2f692281bd1fe82184 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Sat, 27 Jul 2024 12:15:17 -0400
Subject: [PATCH] Start EASY debugging

---
 workflow/templates/easy/EASYconsole.m | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflow/templates/easy/EASYconsole.m b/workflow/templates/easy/EASYconsole.m
index 3257376a..6082fce2 100644
--- a/workflow/templates/easy/EASYconsole.m
+++ b/workflow/templates/easy/EASYconsole.m
@@ -35,11 +35,11 @@ function varargout = EASYconsole(varargin)
   % Set scansDir intelligently (project scans directory)
   % Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY
   % This better enables running the new EASY in standalone mode
-  if exist('PROJECT', 'env') && ~isempty(getenv('PROJECT'))
+  if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
     scansDir=get_env('PROJECT');
     disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
     disp('This usually indicates that we are in standalone mode');
-  elseif exist('SCANS_DIR', 'env') && ~isempty(getenv('SCANS_DIR'))
+  elseif exist('SCANS_DIR', 'var') && ~isempty(getenv('SCANS_DIR'))
     scansDir=get_env('SCANS_DIR');
     disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
     disp('This usually indicates that we are in module mode');
@@ -55,7 +55,7 @@ function varargout = EASYconsole(varargin)
   end
 
   % If we don't have the EASY_SUFFIX from the module, generate it from scansDir
-  if exist('EASY_SUFFIX', 'env') && ~isempty(getenv('EASY_SUFFIX'))
+  if exist('EASY_SUFFIX', 'var') && ~isempty(getenv('EASY_SUFFIX'))
     easySuffix=get_env('EASY_SUFFIX');
   else
     [dirName, ~]=fileparts(scansDir);
@@ -82,7 +82,7 @@ function varargout = EASYconsole(varargin)
   end
 
   % Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode
-  if exist('EASY_DIR','env') && ~isempty(getenv('EASY_DIR'))
+  if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
     EASY_DIR=fullfile(get_env('EASY_DIR'));
     if easyDir ~= EASY_DIR % sanity check
       disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
@@ -94,13 +94,13 @@ function varargout = EASYconsole(varargin)
     disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
   end
 
-  if exist('PROJECT_USER', 'env') && ~isempty(getenv('PROJECT_USER'))
+  if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
     if get_env('PROJECT_USER') ~= userName % sanity check
       disp("WARNING: PROJECT_USER does not match the current namespace");
     end
   end
 
-  if exist('EASY_RESULTS_DIR', 'env') && ~isempty(getenv('EASY_RESULTS_DIR'))
+  if exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR'))
     easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
     disp(strcat('Using output directory: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
   else
@@ -110,7 +110,7 @@ function varargout = EASYconsole(varargin)
     disp(strcat('Using output directory: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
   end
 
-  if exist('MASTER_PLATE_FILE', 'env') && ~isempty(getenv('MASTER_PLATE_FILE'))
+  if exist('MASTER_PLATE_FILE', 'var') && ~isempty(getenv('MASTER_PLATE_FILE'))
     masterPlateFile=fullfile(get_env('MASTER_PLATE_FILE'));
     disp(strcat('Using drug media file: ', masterPlateFile, ' from environment variable MASTER_PLATE_FILE'))
   else
@@ -124,7 +124,7 @@ function varargout = EASYconsole(varargin)
     end
   end
 
-  if exist('DRUG_MEDIA_FILE', 'env') && ~isempty(getenv('DRUG_MEDIA_FILE'))
+  if exist('DRUG_MEDIA_FILE', 'var') && ~isempty(getenv('DRUG_MEDIA_FILE'))
     drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE'));
     disp(strcat('Using drug media file: ', drugMediaFile, ' from environment variable DRUG_MEDIA_FILE'))
   else