From d2fdf4e7c7af98980ccfbba85bd042199a903eeb Mon Sep 17 00:00:00 2001 From: Aaron <aaronquinlan@gmail.com> Date: Fri, 21 Oct 2011 12:02:37 -0400 Subject: [PATCH] Tweaked Makefile for proper zlib inclusion --- src/bamToBed/Makefile | 2 +- src/bedToBam/Makefile | 2 +- src/coverageBed/Makefile | 2 +- src/cuffToTrans/Makefile | 44 ++++++++++++++++++++++++++++++++++ src/genomeCoverageBed/Makefile | 2 +- src/intersectBed/Makefile | 2 +- src/multiBamCov/Makefile | 2 +- src/pairToBed/Makefile | 2 +- src/subtractBed/Makefile | 6 ++++- src/tagBam/Makefile | 2 +- src/windowBed/Makefile | 2 +- 11 files changed, 58 insertions(+), 10 deletions(-) create mode 100644 src/cuffToTrans/Makefile diff --git a/src/bamToBed/Makefile b/src/bamToBed/Makefile index 14ed012a..65741ae8 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 d94d2e87..f6e18c0c 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 a4a4e03f..48ccb37f 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" $(*F).cpp diff --git a/src/cuffToTrans/Makefile b/src/cuffToTrans/Makefile new file mode 100644 index 00000000..6e417369 --- /dev/null +++ b/src/cuffToTrans/Makefile @@ -0,0 +1,44 @@ +UTILITIES_DIR = ../utils/ +OBJ_DIR = ../../obj/ +BIN_DIR = ../../bin/ + +# ------------------- +# define our includes +# ------------------- +INCLUDES = -I$(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 9b8b4788..4194fdb5 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 50ca671a..71cba93d 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 79412902..9313ab95 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 e173500d..9d94beb4 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" $(*F).cpp diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile index 10069702..f67ac7b6 100644 --- a/src/subtractBed/Makefile +++ b/src/subtractBed/Makefile @@ -5,7 +5,11 @@ BIN_DIR = ../../bin/ # ------------------- # define our includes # ------------------- -INCLUDES = -I$(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 b2dbcc4c..35b97a2c 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 f988c40d..0b5303f3 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 -- GitLab