[med-svn] [hilive] 02/02: remove forced CXX flags and add libhts-dev

[Gert Wollny]

This is an automated email from the git hooks/post-receive script.

gert-guest pushed a commit to branch master
in repository hilive.

commit 1cf0055b5cbd581c9d1c28703358c0ad9027f34f
Author: Gert Wollny <gw.fossdev at gmail.com>
Date:   Tue Dec 6 08:01:29 2016 +0000

    remove forced CXX flags and add libhts-dev
---
 CMakeLists.txt                     |  8 ++++----
 debian/changelog                   |  6 +++---
 debian/patches/use_FindSeQan.patch | 12 ++++++++++++
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4c6b203..99d5ae2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,7 +12,7 @@ set (HiLive_VERSION_MINOR 3)
 set (HiLive_K 15 CACHE INT "Set the k-mer length for index and mapper")
 
 # Set flags for compilation
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++11 -O0")
+#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++11 -O0")
 
 
 # configure a header file to pass some of the CMake settings to the source code
@@ -28,8 +28,8 @@ include_directories("${PROJECT_BINARY_DIR}")
 #############################
 ### setup seqan libraries ###
 
-set (CMAKE_MODULE_PATH "/home/schulzeja/masterthesis/tools/seqan-src/util/cmake") # adjust this to [pathToSeqanCode]/util/cmake
-set (SEQAN_INCLUDE_PATH "/home/schulzeja/masterthesis/tools/seqan-src/include/") # adjust this to [pathToSeqanCode]/include
+set (CMAKE_MODULE_PATH "/usr/share/seqan/cmake") # adjust this to [pathToSeqanCode]/util/cmake
+#set (SEQAN_INCLUDE_PATH "/home/schulzeja/masterthesis/tools/seqan-src/include/") # adjust this to [pathToSeqanCode]/include
 
 # Configure SeqAn, enabling features for libbz2 and zlib.
 #set (SEQAN_FIND_DEPENDENCIES ZLIB BZip2) # original version from seqan tutorial
@@ -84,7 +84,7 @@ foreach (x ${LIB_NAMES})
 	list(APPEND LIB_LIST "lib/${x}.cpp")
 endforeach()
 add_library(HiLiveLibs ${LIB_LIST})
-
+set_target_properties(HiLiveLibs PROPERTIES SKIP_BUILD_RPATH TRUE)
 
 #############################
 ### Build the executables ###
diff --git a/debian/changelog b/debian/changelog
index 60a11a6..a0839b3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,12 @@
 hilive (0.3-1) UNRELEASED; urgency=medium
 
   [Andreas Tille]
-  * New upstream location with proper tagging 
+  * New upstream location with proper tagging, Closes: #833392
 
   [Gert Wollny] 
-  * TODO: check whether it closes #833392
-  * d/control: Add libseqan2-dev as build dependency 
+  * d/control: Add libseqan2-dev  and libhts-dev as build dependency 
   * d/patches/use_...: correct path to cmake modules for FindSeQan
+    an remove forced CXXFLAGS 
 
  -- Andreas Tille <tille at debian.org>  Thu, 04 Aug 2016 08:24:34 +0200
 
diff --git a/debian/patches/use_FindSeQan.patch b/debian/patches/use_FindSeQan.patch
index 595c84b..d781c0f 100644
--- a/debian/patches/use_FindSeQan.patch
+++ b/debian/patches/use_FindSeQan.patch
@@ -1,5 +1,17 @@
+Description: remove forced cflags and set proper cmake module path 
+Author: Gert Wollny <gw.fossdev at gmail.com>
+
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
+@@ -12,7 +12,7 @@
+ set (HiLive_K 15 CACHE INT "Set the k-mer length for index and mapper")
+ 
+ # Set flags for compilation
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++11 -O0")
++#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++11 -O0")
+ 
+ 
+ # configure a header file to pass some of the CMake settings to the source code
 @@ -28,8 +28,8 @@
  #############################
  ### setup seqan libraries ###

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hilive.git