diff --git a/.gitignore b/.gitignore
index d0c7436..591288f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,7 @@ src/processing/postprocessing/tSNE/
 us.stackdump
 
 Ontologies/
+
+mccExcludedFiles\.log
+
+*.exe
diff --git a/src/SpectralAnalysis.m b/src/SpectralAnalysis.m
index bab5d59..6ea70a1 100644
--- a/src/SpectralAnalysis.m
+++ b/src/SpectralAnalysis.m
@@ -5,13 +5,14 @@
 if(isdeployed())
     disp('Initialising MATLAB, please wait...');
     path = ctfroot();
+    disp(path);
 else
     path = [fileparts(mfilename('fullpath'))];
+    
+    % Ensure all folders are on the path
+    addpath(genpath(path));
 end
 
-% Ensure all folders are on the path
-addpath(genpath(path));
-
 % Ensure libraries are on the path
 addJARsToClassPath();
 
diff --git a/src/util/getSubclasses.m b/src/util/getSubclasses.m
index 4b3a11d..a447934 100644
--- a/src/util/getSubclasses.m
+++ b/src/util/getSubclasses.m
@@ -2,9 +2,17 @@
     % Get the location of the m file to instigate the search for subclasses
     if(isdeployed())
         spectralAnalysisPath = [ctfroot() filesep 'src' filesep];
+        
+        if(~exist(spectralAnalysisPath, 'file'))
+            spectralAnalysisPath = [ctfroot() filesep 'SpectralAnal' filesep 'src' filesep];
+        end
     else
         spectralAnalysisPath = [fileparts(mfilename('fullpath'))  filesep '..' filesep];
     end
+    
+    if(~exist(spectralAnalysisPath, 'file'))
+        disp(['Couldn''t find the SpectralAnalysis path: ' spectralAnalysisPath]);
+    end
         
     % Limit the locations to speed up the search when looking for specific
     % types