[med-svn] [crac] 01/01: Use debian packaged libs

[Andreas Tille]

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tille pushed a commit to branch master
in repository crac.

commit 209a11c982792ddec00f64755c910bd2d02f7677
Author: Andreas Tille <tille at debian.org>
Date:   Sun Sep 11 14:36:13 2016 +0200

    Use debian packaged libs
---
 debian/patches/series                              |  2 ++
 .../patches/use_debian_packaged_libgzstream.patch  | 25 +++++++++++++++++++++
 .../patches/use_debian_packaged_libjellyfish.patch | 26 ++++++++++++++++++++++
 3 files changed, 53 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..2956b70
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+use_debian_packaged_libgzstream.patch
+use_debian_packaged_libjellyfish.patch
diff --git a/debian/patches/use_debian_packaged_libgzstream.patch b/debian/patches/use_debian_packaged_libgzstream.patch
new file mode 100644
index 0000000..12802a0
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libgzstream.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-update: Sat, 10 Sep 2016 23:41:37 +0200
+Description: Use Debian packaged libgzstream
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -374,7 +374,6 @@ AC_CONFIG_FILES([\
+   control crac.spec                             \
+   Makefile src/Makefile scripts/Makefile        \
+   src/libReadsInfo/Makefile src/libSSA/Makefile \
+-  src/libgzstream/Makefile                      \
+   src/libReadsReader/Makefile                   \
+   src/libReadsReader/kseq/Makefile              \
+   man/Makefile man/crac.1                       \
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -105,7 +105,7 @@ CRAC_LINKS = crac-index
+ all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
+ 
+ 
+-SUBDIRS = libReadsInfo libSSA libgzstream libReadsReader
++SUBDIRS = libReadsInfo libSSA libReadsReader
+ if INCLUDED_GKARRAYS
+   SUBDIRS += libGkArrays
+ endif
diff --git a/debian/patches/use_debian_packaged_libjellyfish.patch b/debian/patches/use_debian_packaged_libjellyfish.patch
new file mode 100644
index 0000000..068e64a
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libjellyfish.patch
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at 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
+@@ -109,9 +109,6 @@ 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         \
+@@ -147,8 +144,8 @@ AM_LDFLAGS = -lm -lpthread -lhts -lSSA -
+ AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bwt -I at abs_srcdir@/libgzstream 
+ 
+ if INCLUDED_JELLYFISH
+-  AM_LDFLAGS += -L at abs_builddir@/libJellyfish-2.0/.libs
+-  AM_CPPFLAGS += -I at abs_srcdir@/libJellyfish-2.0/include
++  AM_LDFLAGS += -ljellyfish-2.0
++  AM_CPPFLAGS += -I/usr/include/jellyfish
+   AM_CXXFLAGS = -std=c++0x
+ endif
+ 

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