Description: Includepaths
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,6 @@
 #---Begin configuration---#
 #---Begin configuration---#
 
-prefix=/usr/local
 AGN_LINK=https://github.com/standage/AEGeAn
 AGN_DATE=2014
 AGN_VERSION=0.10.1
@@ -36,7 +35,7 @@
 
 # Compilation settings
 CC=gcc
-CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
+CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
 GTFLAGS=prefix=$(prefix)
 ifeq ($(cairo),no)
   CFLAGS += -DWITHOUT_CAIRO
@@ -60,7 +59,7 @@
 ifdef lib
   LDFLAGS += -L$(lib)
 endif
-INCS=-I src/genometools/src -I src/genometools/obj -I /usr/local/include/genometools \
+INCS=-I src/genometools/src -I src/genometools/obj -I /usr/include/genometools \
      -I inc/core -I inc/ParsEval -I inc/VAnG       \
      -I /usr/include/cairo -I /sw/include/cairo
 ifeq ($(memcheck),yes)
@@ -76,22 +75,23 @@
 		
 
 install:	all
-		@- test -d $(prefix)/bin || mkdir $(prefix)/bin
-		cp $(PE_EXE) $(XT_EXE) $(LP_EXE) $(prefix)/bin/.
-		cp libaegean.a $(prefix)/lib/.
-		@- test -d $(prefix)/include/aegean || mkdir $(prefix)/include/aegean
+		@- test -d $(prefix)/bin || mkdir -p $(prefix)/bin
+		cp $(PE_EXE) $(XT_EXE) $(LP_EXE) $(prefix)/bin/
+	  @- test -d $(prefix)/lib || mkdir -p $(prefix)/lib
+		cp libaegean.a $(prefix)/lib/
+		@- test -d $(prefix)/include/aegean || mkdir -p $(prefix)/include/aegean
 		@- rm -f $(prefix)/include/aegean/*
-		cp inc/core/*.h $(prefix)/include/aegean/.
-		@- test -d $(prefix)/share || mkdir $(prefix)/share
-		@- test -d $(prefix)/share/aegean || mkdir $(prefix)/share/aegean
-		cp -r data/share/* $(prefix)/share/aegean/.
+		cp inc/core/*.h $(prefix)/include/aegean/
+		@- test -d $(prefix)/share || mkdir -p $(prefix)/share
+		@- test -d $(prefix)/share/aegean || mkdir -p $(prefix)/share/aegean
+		cp -r data/share/* $(prefix)/share/aegean/
 
 uninstall:	
 		rm -r $(prefix)/$(PE_EXE)
 		rm -r $(prefix)/share/parseval
 
 clean:		
-		rm -rf $(BINS) $(UT_EXE) libaegean.a $(CLSS_MDL_OBJS) inc/core/AgnVersion.h bin/*.dSYM
+		rm -rf README $(BINS) $(UT_EXE) libaegean.a $(CLSS_MDL_OBJS) inc/core/AgnVersion.h bin/*.dSYM
 
 $(AGN_OBJS):	obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
 		@- mkdir -p obj
