[med-svn] [hilive] 03/03: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository hilive.

commit 6061b615d5e02e4853811c484ebe88328d18b3f8
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 22 09:58:21 2017 +0200

    Adapt patches
---
 debian/patches/do_not_set_rpath.patch |  2 +-
 debian/patches/use_FindSeQan.patch    | 25 ++++++++++++-------------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/debian/patches/do_not_set_rpath.patch b/debian/patches/do_not_set_rpath.patch
index 5c52fdf..e64f11a 100644
--- a/debian/patches/do_not_set_rpath.patch
+++ b/debian/patches/do_not_set_rpath.patch
@@ -7,7 +7,7 @@ Description: Do not set rpath
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -84,7 +84,7 @@ foreach (x ${LIB_NAMES})
+@@ -62,7 +62,7 @@ foreach (x ${LIB_NAMES})
  	list(APPEND LIB_LIST "lib/${x}.cpp")
  endforeach()
  add_library(HiLiveLibs ${LIB_LIST})
diff --git a/debian/patches/use_FindSeQan.patch b/debian/patches/use_FindSeQan.patch
index 32af7bf..3b0e83e 100644
--- a/debian/patches/use_FindSeQan.patch
+++ b/debian/patches/use_FindSeQan.patch
@@ -3,24 +3,23 @@ Author: Gert Wollny <gw.fossdev at gmail.com>
 
 --- 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")
+@@ -9,7 +9,7 @@ add_definitions(-DHiLive_VERSION_MAJOR=1
+ add_definitions(-DHiLive_VERSION_MINOR=0)
  
  # 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")
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++14 -O0")
++#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++14 -O0")
  
- 
- # configure a header file to pass some of the CMake settings to the source code
-@@ -28,8 +28,9 @@ include_directories("${PROJECT_BINARY_DI
+ # add the binary tree to the search path for include files
+ include_directories("${PROJECT_BINARY_DIR}")
+@@ -38,8 +38,8 @@ set(CompressionLibs "${ZLIB_LIBRARIES};l
  #############################
- ### setup seqan libraries ###
+ ### setup seqan libraries ### needs to be done AFTER searching for Zlib
  
--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 (SeqAn_DIR "/usr/share/cmake")
-+set (CMAKE_MODULE_PATH "/usr/share/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/local/lib/seqan/util/cmake") # adjust this to [pathToSeqanCode]/util/cmake
+-set (SEQAN_INCLUDE_PATH "/usr/local/lib/seqan/include/") # adjust this to [pathToSeqanCode]/include
++set (CMAKE_MODULE_PATH "/usr/share/cmake/") # adjust this to [pathToSeqanCode]/util/cmake
++set (SEQAN_INCLUDE_PATH "/usr/lib/seqan/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

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