gentoo-overlay/sci-biology/express/files/express-1.5.1-buildsystem.patch

 CMakeLists.txt     | 8 +++-----
 src/CMakeLists.txt | 4 ++--
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c768e28..65d5633 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
 set(${PROJECT_NAME}_VERSION_MINOR 5)
 set(${PROJECT_NAME}_VERSION_PATCH 1)
 
-set(CMAKE_CXX_FLAGS "-Wall")
-
 set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}")
 
 set(CMAKE_BUILD_TYPE Release)
-set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_STATIC_LIBS OFF)
 
 find_package(Boost 1.39
     COMPONENTS
@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
 
 find_package(Protobuf)
 if (PROTOBUF_FOUND)
-  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
+  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE})
 	set(PROTO_INT 1)
 else (PROTOBUF_FOUND)
-  include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
+  include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE})
 	set(PROTO_INT 0)
 endif(PROTOBUF_FOUND)
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1cc0c01..8929d1f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC)
 if(WIN32)
   set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
 else(WIN32)
-  set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread")
+  set(LIBRARIES ${LIBRARIES} "bamtools" "pthread")
 endif(WIN32)
 
 if (PROTOBUF_FOUND)
-  set(LIBRARIES ${LIBRARIES} "libprotobuf.a")
+  set(LIBRARIES ${LIBRARIES} "protobuf")
 endif(PROTOBUF_FOUND)
 
 target_link_libraries(express ${LIBRARIES})