diff --git a/lib/metric_fu/metric.rb b/lib/metric_fu/metric.rb
index 267e11156..e3c349800 100644
--- a/lib/metric_fu/metric.rb
+++ b/lib/metric_fu/metric.rb
@@ -43,10 +43,11 @@ def default_run_args
       run_options.map { |k, v| "--#{k} #{v}" }.join(" ")
     end
 
-    def run
+    def run(options = run_options)
       not_implemented
     end
 
+    # TODO: move into generator
     def run_external(args = default_run_args)
       runner = GemRun.new(
         gem_name: gem_name.to_s,
diff --git a/lib/metric_fu/metrics/flay/generator.rb b/lib/metric_fu/metrics/flay/generator.rb
index aaba47782..c02a35e3b 100644
--- a/lib/metric_fu/metrics/flay/generator.rb
+++ b/lib/metric_fu/metrics/flay/generator.rb
@@ -5,8 +5,7 @@ def self.metric
     end
 
     def emit
-      args =  "#{minimum_duplication_mass} #{dirs_to_flay}"
-      @output = run!(args)
+      @output = run(options)
     end
 
     def analyze
@@ -35,17 +34,27 @@ def calculate_result(matches)
       }
     end
 
+    def run(options)
+      flay_options = Flay.default_options.merge(minimum_duplication_mass)
+      flay = Flay.new flay_options
+      files = Flay.expand_dirs_to_files(dirs_to_flay)
+      flay.process(*files)
+      MetricFu::Utility.capture_output do
+         flay.report
+      end
+    end
+
     private
 
     def minimum_duplication_mass
       flay_mass = options[:minimum_score]
-      return "" unless flay_mass
+      return {} unless flay_mass
 
-      "--mass #{flay_mass} "
+      { :mass => flay_mass }
     end
 
     def dirs_to_flay
-      options[:dirs_to_flay].join(" ")
+      options[:dirs_to_flay]
     end
   end
 end
diff --git a/lib/metric_fu/metrics/flay/metric.rb b/lib/metric_fu/metrics/flay/metric.rb
index 67258e1bc..8eba709ff 100644
--- a/lib/metric_fu/metrics/flay/metric.rb
+++ b/lib/metric_fu/metrics/flay/metric.rb
@@ -22,6 +22,7 @@ def enable
     end
 
     def activate
+      activate_library 'flay'
       super
     end
   end
diff --git a/spec/metric_fu/metrics/flay/generator_spec.rb b/spec/metric_fu/metrics/flay/generator_spec.rb
index 2336bb750..4b6c2e13f 100644
--- a/spec/metric_fu/metrics/flay/generator_spec.rb
+++ b/spec/metric_fu/metrics/flay/generator_spec.rb
@@ -8,7 +8,10 @@
       allow(File).to receive(:directory?).and_return(true)
       @flay = MetricFu::FlayGenerator.new(options)
 
-      expect(@flay).to receive(:run!).with(" app lib")
+      expected_options = Flay.default_options
+      expect(Flay).to receive(:expand_dirs_to_files).with(options[:dirs_to_flay])
+      flay = double('flay', :process => nil)
+      allow(Flay).to receive(:new).and_return(flay)
       output = @flay.emit
     end
 
@@ -17,7 +20,9 @@
       allow(File).to receive(:directory?).and_return(true)
       @flay = MetricFu::FlayGenerator.new(options)
 
-      expect(@flay).to receive(:run!).with("--mass 99  ")
+      expected_options = Flay.default_options.merge(:mass => 99)
+      flay = double('flay', :process => nil)
+      expect(Flay).to receive(:new).with(expected_options).and_return(flay)
       output = @flay.emit
     end
   end