diff --git a/src/bamToBed/Makefile b/src/bamToBed/Makefile
index 14ed012a9933b50de03940de270c9f75243807f4..65741ae8f4e4e5bef22438b5b2f45746e22ab5fa 100644
--- a/src/bamToBed/Makefile
+++ b/src/bamToBed/Makefile
@@ -31,7 +31,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/bedToBam/Makefile b/src/bedToBam/Makefile
index d94d2e87d6b8af713fffedc5e2e0a2d9f503a7b8..f6e18c0c1df051d8b33d214db1cbdf8d5ef389aa 100644
--- a/src/bedToBam/Makefile
+++ b/src/bedToBam/Makefile
@@ -32,7 +32,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile
index a4a4e03ffb64c6d17958e0313f52cd233bed6fef..48ccb37fa903f4c79e2ee69aa957237b09295744 100644
--- a/src/coverageBed/Makefile
+++ b/src/coverageBed/Makefile
@@ -30,7 +30,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/cuffToTrans/Makefile b/src/cuffToTrans/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..6e417369a1cd5f4a15ec1c39c99b6ed405cfe11c
--- /dev/null
+++ b/src/cuffToTrans/Makefile
@@ -0,0 +1,44 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= cuffToTransMain.cpp cuffToTrans.cpp Fasta.cpp split.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= cuffToTrans
+
+
+all: $(PROGRAM)
+
+.PHONY: all
+
+$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+	@echo "  * linking $(PROGRAM)"
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
+		
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 9b8b4788e71f7bde2fb618437d4866d53bba115f..4194fdb581eecaef89964490ddb8c4f146270593 100644
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -30,7 +30,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile
index 50ca671a6f831b02cad9e40291e1b9805b59b4d2..71cba93dd95b06e319ad3d2621874859985373fc 100644
--- a/src/intersectBed/Makefile
+++ b/src/intersectBed/Makefile
@@ -31,7 +31,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)  -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/multiBamCov/Makefile b/src/multiBamCov/Makefile
index 7941290229f72e9853c02a999f95bb21d037ea99..9313ab959e995bdeea6427c29eb42924045826c1 100644
--- a/src/multiBamCov/Makefile
+++ b/src/multiBamCov/Makefile
@@ -28,7 +28,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/pairToBed/Makefile b/src/pairToBed/Makefile
index e173500dc86e50a5c5badb31e51c5032307939a8..9d94beb499169cbaec07b1ee36ea5f28ed44ac14 100644
--- a/src/pairToBed/Makefile
+++ b/src/pairToBed/Makefile
@@ -30,7 +30,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)  -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile
index 10069702f652cd032bb630572397e38deffb8437..f67ac7b666bf3ed697b4e282bcc0c13708e33903 100644
--- a/src/subtractBed/Makefile
+++ b/src/subtractBed/Makefile
@@ -5,7 +5,11 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+           -I$(UTILITIES_DIR)/lineFileUtilities/ \
+           -I$(UTILITIES_DIR)/version/ \
+           -I$(UTILITIES_DIR)/gzstream/ \
+           -I$(UTILITIES_DIR)/fileType/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/tagBam/Makefile b/src/tagBam/Makefile
index b2dbcc4c1561cd1df34b6166a344d7f2b204b873..35b97a2cc093abd757eef86be6c3a53f0ff69ebf 100644
--- a/src/tagBam/Makefile
+++ b/src/tagBam/Makefile
@@ -30,7 +30,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)  -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/windowBed/Makefile b/src/windowBed/Makefile
index f988c40d09580e6ee8f6c1e7e51c9555f236c4e0..0b5303f3980c228c20294d984af3676877dc8e91 100644
--- a/src/windowBed/Makefile
+++ b/src/windowBed/Makefile
@@ -30,7 +30,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)   -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp