[med-svn] [crac] 04/07: use_debian_packages_libgtarrays.patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository crac.

commit 2e055b365ae2df6a28388c6791e55d524612e06c
Author: Andreas Tille <tille at debian.org>
Date:   Mon Sep 12 15:38:52 2016 +0200

    use_debian_packages_libgtarrays.patch
---
 debian/patches/series                              |  1 +
 .../patches/use_debian_packages_libgtarrays.patch  | 50 ++++++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 90d2206..bc6bee1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ use_debian_packaged_libgzstream.patch
 use_debian_packaged_libjellyfish.patch
 fix_includes.patch
 skip_failed_test_bug-14958.patch
+use_debian_packages_libgtarrays.patch
diff --git a/debian/patches/use_debian_packages_libgtarrays.patch b/debian/patches/use_debian_packages_libgtarrays.patch
new file mode 100644
index 0000000..66a80a0
--- /dev/null
+++ b/debian/patches/use_debian_packages_libgtarrays.patch
@@ -0,0 +1,50 @@
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -106,9 +106,6 @@ all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
+ 
+ 
+ SUBDIRS = libReadsInfo libSSA libReadsReader
+-if INCLUDED_GKARRAYS
+-  SUBDIRS += libGkArrays
+-endif
+ 
+ crac_SOURCES =                    \
+   basic.h const.h types.h         \
+@@ -150,11 +147,11 @@ if INCLUDED_JELLYFISH
+ endif
+ 
+ if INCLUDED_GKARRAYS
+-  AM_LDFLAGS += -L at abs_builddir@/libGkArrays/src/.libs
+-  AM_CPPFLAGS += -I at abs_srcdir@/libGkArrays/src/
++  AM_LDFLAGS += `pkg-config --libs libGkArrays`
++  AM_CPPFLAGS += `pkg-config --cflags libGkArrays`
+ if INCLUDED_PROGRESSBAR
+-  AM_LDFLAGS += -L at abs_builddir@/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+-  AM_CPPFLAGS += -I at abs_srcdir@/libGkArrays/src/libProgressBar-1.2.0/
++  AM_LDFLAGS += `pkg-config --libs libProgressBar`
++  AM_CPPFLAGS += `pkg-config --cflags libProgressBar`
+ endif
+ endif
+ 
+--- a/src/libReadsInfo/Makefile.am
++++ b/src/libReadsInfo/Makefile.am
+@@ -124,7 +124,7 @@ libReadsInfo_a_SOURCES =
+ 
+ libReadsInfo_a_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_top_srcdir@/src -I at abs_top_srcdir@/src/libSSA 
+ if INCLUDED_GKARRAYS
+-  libReadsInfo_a_CPPFLAGS += -I at abs_srcdir@/../libGkArrays/src/
++  libReadsInfo_a_CPPFLAGS += `pkg-config --cflags libGkArrays`
+ endif
+ 
+ 
+--- a/src/libSSA/Makefile.am
++++ b/src/libSSA/Makefile.am
+@@ -101,7 +101,7 @@
+ bin_PROGRAMS = crac-index
+ crac_index_SOURCES = cracIndex.cpp cracIndex.h
+ 
+-AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@/karkkainen_bwt -I at abs_top_srcdir@/src/libGkArrays/src
++AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@/karkkainen_bwt `pkg-config --cflags libGkArrays`
+ AM_LDFLAGS = -lm -lpthread -lSSA -L at abs_builddir@/
+ LDADD = libSSA.a
+ 

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