Author: Andreas Tille <tille@debian.org>
Last-update: Sat, 10 Sep 2016 23:41:37 +0200
Description: Use Debian packaged libjellyfish-2.0

--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -111,9 +111,6 @@ SUBDIRS = libReadsInfo libSSA libReadsRe
 if INCLUDED_GKARRAYS
   SUBDIRS += libGkArrays
 endif
-if INCLUDED_JELLYFISH
-  SUBDIRS += libJellyfish-2.0
-endif
 
 crac_SOURCES =                    \
   basic.h const.h types.h         \
@@ -149,8 +146,8 @@ AM_LDFLAGS = -lm -lpthread -lhts -lSSA -
 AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@ -I@abs_srcdir@/libSSA -I@abs_srcdir@/libSSA/karkkainen_bw
 
 if INCLUDED_JELLYFISH
-  AM_LDFLAGS += -L@abs_builddir@/libJellyfish-2.0/.libs
-  AM_CPPFLAGS += -I@abs_srcdir@/libJellyfish-2.0/include
+  AM_LDFLAGS += -ljellyfish-2.0
+  AM_CPPFLAGS += -I/usr/include/jellyfish
   AM_CXXFLAGS = -std=c++0x
 endif