X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=bowtie.git;a=blobdiff_plain;f=debian%2Fpatches%2Fuse_debian_seqan.patch;fp=debian%2Fpatches%2Fuse_debian_seqan.patch;h=53c9519e8dd6f069ac2c15afa8c37eb1bad072f3;hp=0000000000000000000000000000000000000000;hb=7ff6d33630733772d810e0ad76ed0a6ff60d612d;hpb=3cce4167a5b99fda4b9b372ee73494ed36dbcd59

diff --git a/debian/patches/use_debian_seqan.patch b/debian/patches/use_debian_seqan.patch
new file mode 100644
index 0000000..53c9519
--- /dev/null
+++ b/debian/patches/use_debian_seqan.patch
@@ -0,0 +1,26 @@
+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)