diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index 53d070285a..25f8a54801 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -87,7 +87,7 @@ def task_status
 
   def populate_template
     uploaded_file = params[:template_json_file]
-    dir = Rails.root.join('config', 'default_data', 'source_types')
+    dir = Rails.root.join('filestore', 'source_types')
 
     if Dir.exist?(dir)
       `rm #{dir}/*`
@@ -146,11 +146,11 @@ def set_status
   end
 
   def lockfile
-    Rails.root.join('tmp', 'populate_templates.lock')
+    Rails.root.join('tmp', 'cache', 'populate_templates.lock')
   end
 
   def resultfile
-    Rails.root.join('tmp', 'populate_templates.result')
+    Rails.root.join('tmp', 'cache', 'populate_templates.result')
   end
 
   def running!
diff --git a/lib/seek/isa_templates/template_extractor.rb b/lib/seek/isa_templates/template_extractor.rb
index b0487a7e24..3f70d1cd70 100644
--- a/lib/seek/isa_templates/template_extractor.rb
+++ b/lib/seek/isa_templates/template_extractor.rb
@@ -12,7 +12,7 @@ def self.extract_templates
         disable_authorization_checks do
           client = Ebi::OlsClient.new
           project = Project.find_or_create_by(title: 'Default Project')
-          directory = Rails.root.join('config', 'default_data', 'source_types')
+          directory = Rails.root.join('filestore', 'source_types')
           directory_files = Dir.exist?(directory) ? Dir.glob("#{directory}/*.json") : []
           raise '<ul><li>Make sure to upload files that have the ".json" extension.</li></ul>' if directory_files == []
 
@@ -172,11 +172,11 @@ def self.seed_isa_tags
       end
 
       def self.lockfile
-        Rails.root.join('tmp', 'populate_templates.lock')
+        Rails.root.join('tmp', 'cache', 'populate_templates.lock')
       end
 
       def self.resultfile
-        Rails.root.join('tmp', 'populate_templates.result')
+        Rails.root.join('tmp', 'cache', 'populate_templates.result')
       end
     end
   end