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Makefile
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Makefile
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BAMTOOLS_ROOT=/srv/gsfs0/projects/curtis/ruping/tools/bamtools/
ZLIB_ROOT=/srv/gsfs0/projects/curtis/ruping/tools/zlib/current/
BOOST_ROOT=/srv/gsfs0/projects/curtis/ruping/tools/boost/current/
CXX=g++
BAMFLAGS=-lbamtools
CXXFLAGS=-lz
LBFLAGS=-Wl,-rpath,$(BAMTOOLS_ROOT)/lib/lib/:$(BOOST_ROOT)/lib
BOOSTFLAGS=-lboost_regex
PREFIX=$(CURDIR)
SRC=$(CURDIR)/src
TOOLSB=$(CURDIR)/utils/
BIN=/bin/
SOURCE_STA=Rseq_bam_stats.cpp
SOURCE_MFV=mappingFlankingVariants.cpp
SOURCE_REC=novelSnvFilter_ACGT.cpp
SOURCE_GS=grep_starts.cpp
STA=Rseq_bam_stats
MFV=mappingFlankingVariants
REC=novelSnvFilter_ACGT
GS=grep_starts
all: Rseq_bam_stats mappingFlankingVariants novelSnvFilter_ACGT grep_starts perl_scripts R_scripts lutils
.PHONY: all
Rseq_bam_stats:
@mkdir -p $(PREFIX)/$(BIN)
@echo "* compiling" $(SOURCE_STA)
@$(CXX) $(SRC)/$(SOURCE_STA) -o $(PREFIX)/$(BIN)/$(STA) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/ -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/
mappingFlankingVariants:
@echo "* compiling" $(SOURCE_MFV)
@$(CXX) $(SRC)/$(SOURCE_MFV) -o $(PREFIX)/$(BIN)/$(MFV) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/ -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/
novelSnvFilter_ACGT:
@echo "* compiling" $(SOURCE_REC)
@$(CXX) $(SRC)/$(SOURCE_REC) -o $(PREFIX)/$(BIN)/$(REC) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/ -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/
grep_starts:
@echo "* compiling" $(SOURCE_GS)
@$(CXX) $(SRC)/$(SOURCE_GS) -o $(PREFIX)/$(BIN)/$(GS) $(BAMFLAGS) $(CXXFLAGS) $(LBFLAGS) $(BOOSTFLAGS) -I $(BAMTOOLS_ROOT)/include/ -I $(ZLIB_ROOT)/include/ -I $(BOOST_ROOT)/include/ -L $(BAMTOOLS_ROOT)/lib/ -L $(ZLIB_ROOT)/lib/ -L $(BOOST_ROOT)/lib/
perl_scripts:
@echo "* copying perl scripts"
@cp $(SRC)/*.pl $(PREFIX)/$(BIN)/
@echo "* done."
R_scripts:
@echo "* copying R scripts"
@cp $(SRC)/*.R $(PREFIX)/$(BIN)/
@echo "* done."
lutils:
@echo "* link utils"
@ln -s $(TOOLSB)/* $(PREFIX)/$(BIN)/
@echo "* done."
DTrace:
@echo "* copying DTrace.pl"
@cp $(SRC)/DTrace.pl $(PREFIX)/$(BIN)/
@echo "* done."
clean:
@echo "Cleaning up everthing."
@rm -rf $(PREFIX)/$(BIN)/
.PHONY: clean