Make sure we build the software the Debian way.
diff --git a/CometSearch/Makefile b/CometSearch/Makefile
index 0ccd9dc..c62115b 100644
--- a/CometSearch/Makefile
+++ b/CometSearch/Makefile
@@ -1,7 +1,7 @@
-CXX = g++
-GCC = gcc
 MSTOOLKIT = ../MSToolkit
-override CXXFLAGS += -O3 -fpermissive -Wall -Wextra -Wno-write-strings -static -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -I. -I$(MSTOOLKIT)/include
+
+# By Filippo Rusconi: -D__LINUX__ is required by the mzParser.h file in /usr/include/libmstoolkit
+override CXXFLAGS += -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit
 
 COMETSEARCH = Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o
 
@@ -15,7 +15,7 @@ Threading.o:          Threading.cpp Threading.h
 	${CXX} ${CXXFLAGS} Threading.cpp -c
 CometSearch.o:        CometSearch.cpp Common.h CometData.h CometDataInternal.h CometSearch.h CometInterfaces.h ThreadPool.h
 	${CXX} ${CXXFLAGS} CometSearch.cpp -c
-CometPreprocess.o:    CometPreprocess.cpp Common.h CometData.h CometDataInternal.h CometPreprocess.h CometInterfaces.h $(MSTOOLKIT)
+CometPreprocess.o:    CometPreprocess.cpp Common.h CometData.h CometDataInternal.h CometPreprocess.h CometInterfaces.h
 	${CXX} ${CXXFLAGS} CometPreprocess.cpp -c
 CometMassSpecUtils.o: CometMassSpecUtils.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometInterfaces.h
 	${CXX} ${CXXFLAGS} CometMassSpecUtils.cpp -c