Description: Use build flags from environment (dpkg-buildflags).
 Necessary for hardening flags.
Author: Simon Ruderich <simon@ruderich.org>
Last-Update: 2012-04-24
Bug-Closed: http://bugs.debian.org/670230

--- bowtie-0.12.7.orig/Makefile
+++ bowtie-0.12.7/Makefile
@@ -177,7 +177,7 @@
   cat $^ | md5sum | awk '{print $$1}' > .$@.md5
 endef
 
-ALL_FLAGS=$(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
+ALL_FLAGS=$(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
 DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
 RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""