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CXX = g++
MSTOOLKIT = mstoolkit
COMETSEARCH = CometSearch
override CXXFLAGS += -O3 -Wall -Wextra -Wno-char-subscripts -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/lib$(MSTOOLKIT) -I$(COMETSEARCH)
EXECNAME = comet-ms
OBJS = Comet.o
DEPS = CometSearch/CometData.h CometSearch/CometDataInternal.h CometSearch/CometPreprocess.h CometSearch/CometWriteOut.h CometSearch/CometWriteSqt.h CometSearch/OSSpecificThreading.h CometSearch/CometMassSpecUtils.h CometSearch/CometSearch.h CometSearch/CometCheckForUpdates.h CometSearch/CometWritePepXML.h CometSearch/CometWriteTxt.h CometSearch/Threading.h CometSearch/CometPostAnalysis.h CometSearch/CometSearchManager.h CometSearch/CometWritePercolator.h CometSearch/Common.h CometSearch/ThreadPool.h CometSearch/CometMassSpecUtils.cpp CometSearch/CometSearch.cpp CometSearch/CometCheckForUpdates.cpp CometSearch/CometWritePepXML.cpp CometSearch/CometWriteTxt.cpp CometSearch/CometPostAnalysis.cpp CometSearch/CometSearchManager.cpp CometSearch/CometWritePercolator.cpp CometSearch/Threading.cpp CometSearch/CometPreprocess.cpp CometSearch/CometWriteOut.cpp CometSearch/CometWriteSqt.cpp
OBJ_DEPS = CometSearch/CometMassSpecUtils.cpp CometSearch/CometSearch.cpp CometSearch/CometCheckForUpdates.cpp CometSearch/CometWritePepXML.cpp CometSearch/CometWriteTxt.cpp CometSearch/CometPostAnalysis.cpp CometSearch/CometSearchManager.cpp CometSearch/CometWritePercolator.cpp CometSearch/Threading.cpp CometSearch/CometPreprocess.cpp CometSearch/CometWriteOut.cpp CometSearch/CometWriteSqt.cpp
LIBPATHS = -L/usr/lib
LIBS = -lmstoolkitlite -lm -lpthread
LIBPATHS = -L$(MSTOOLKIT) -L$(COMETSEARCH)
LIBS = -lcometsearch -lmstoolkitlite -lm -lpthread
comet-ms: $(OBJS)
cd CometSearch ; make
echo "done"
${CXX} $(CXXFLAGS) $(OBJ_DEPS) $(OBJS) $(LIBPATHS) $(LIBS) -o ${EXECNAME}
Comet.o: Comet.cpp $(OBJ_DEPS)
${CXX} ${CXXFLAGS} $(OBJ_DEPS) Comet.cpp -c
clean:
rm -f *.o ${EXECNAME}
cd CometSearch ; make clean
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