Description: Assorted patches
  * Set paths to hhsuite components for Perl scripts.
  * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq .
Author: Laszlo Kajan <lkajan@rostlab.org>
--- a/src/Makefile
+++ b/src/Makefile
@@ -14,13 +14,13 @@ endif
 
 ifdef ICC
   CXX = env LANG=C icc
-  CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) -I$(FFINDEX_DIR)
+  CXXFLAGS += -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR)
   HHSEARCH_LIBS = -lpthread -lrt
   HHBLITS_LIBS = -lpthread -lrt -openmp
   OBJECT_LIBS = -openmp
 else # ifndef ICC
   CXX = g++
-  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -fopenmp
+  CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp
   HHSEARCH_LIBS = -lpthread
   HHBLITS_LIBS = -lpthread -fopenmp
   HHALIGN_LIBS = 
@@ -51,7 +51,7 @@ else # ifndef ICC
   endif
 endif # ifndef ICC
 
-CPP = $(CXX) $(CXXFLAGS)
+CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)
 CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)
 
 
@@ -92,7 +92,7 @@ hhsearch_valgrind: hhsearch.C $(SOURCES)
 	  $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
 
 hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
-	 $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
+	 $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex
 
 hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
 	 $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
