--- /dev/null
+Note: This patch is deactivated because the Debian packaged version of SeqAn 1.2
+ is not compatible with the version included into this package
+
+Author: Andreas Tille <tilleqdebian.org>
+Date: 2011-01-30
+Description: Use Debian packages SeqAn Librariy instead of copy in upstream source
+--- bowtie-0.12.7.orig/Makefile
++++ bowtie-0.12.7/Makefile
+@@ -2,7 +2,7 @@
+ # Makefile for bowtie, bowtie-build, bowtie-inspect
+ #
+
+-SEQAN_DIR = SeqAn-1.1
++SEQAN_DIR = /usr/include/seqan
+ SEQAN_INC = -I $(SEQAN_DIR)
+ INC = $(SEQAN_INC)
+ GCC_PREFIX = $(shell dirname `which gcc`)
+@@ -149,8 +149,6 @@
+ $(wildcard *.hh) \
+ $(wildcard *.c) \
+ $(wildcard *.cpp) \
+- $(shell $(FIND) SeqAn-1.1 -name "*.h") \
+- $(shell $(FIND) SeqAn-1.1 -name "*.txt") \
+ doc/strip_markdown.pl \
+ Makefile \
+ $(GENERAL_LIST)