Tweaked Makefile for proper zlib inclusion

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

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

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

src/cuffToTrans/Makefile

+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

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

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

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

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

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

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

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