--- bowtie-1.2.2/Makefile	2019-02-18 13:26:29.490835084 +0100
+++ bowtie-1.2.2/Makefile	2019-02-18 13:28:36.864742545 +0100
@@ -5,10 +5,7 @@
 prefix = /usr/local
 bindir = $(prefix)/bin
 
-SEQAN_DIR = ./SeqAn-1.1
-# treat SeqAn as a sysdir to suppress warnings
-SEQAN_INC = -isystem $(SEQAN_DIR)
-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
 CPP = g++
 CXX = $(CPP)
 CC = gcc