debian/control

@@ -6,7 +6,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
                cmake,
-               libgatbcore-dev,
+               libgatbcore-dev (>= 1.4.1+git20180206.6f8fce8~),
                libboost-dev,
                libhdf5-dev,
                zlib1g-dev

debian/patches/use_debian_packaged_gatb-core.patch

@@ -15,3 +15,64 @@ Description: Use cmake input file of Debian packaged gatb-core
  
  ################################################################################
  # THIRD PARTIES
+--- a/tools/QHC/CMakeLists.txt
++++ b/tools/QHC/CMakeLists.txt
+@@ -22,7 +22,9 @@ set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BIN
+ 
+ 
+ # we define which libraries to be linked with project binary
+-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
++include(GNUInstallDirs)
++LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
++target_link_libraries (${PROJECT_NAME} gatbcore hdf5 )
+ 
+ 
+ # We copy the project binary to the 'bin' directory
+--- a/tools/kissnp2/CMakeLists.txt
++++ b/tools/kissnp2/CMakeLists.txt
+@@ -22,8 +22,10 @@ set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BIN
+ 
+ 
+ # we define which libraries to be linked with project binary
+-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
++include(GNUInstallDirs)
++LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
++target_link_libraries (${PROJECT_NAME} gatbcore hdf5 )
+ 
+ 
+ # We copy the project binary to the 'bin' directory
+-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+\ No newline at end of file
++INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+--- a/tools/kissreads2/CMakeLists.txt
++++ b/tools/kissreads2/CMakeLists.txt
+@@ -22,8 +22,10 @@ set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BIN
+ 
+ 
+ # we define which libraries to be linked with project binary
+-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
++include(GNUInstallDirs)
++LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
++target_link_libraries (${PROJECT_NAME} gatbcore hdf5 )
+ 
+ 
+ # We copy the project binary to the 'bin' directory
+-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+\ No newline at end of file
++INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+--- a/tools/read_file_names/CMakeLists.txt
++++ b/tools/read_file_names/CMakeLists.txt
+@@ -22,8 +22,10 @@ set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BIN
+ 
+ 
+ # we define which libraries to be linked with project binary
+-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
++include(GNUInstallDirs)
++LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
++target_link_libraries (${PROJECT_NAME} gatbcore hdf5 )
+ 
+ 
+ # We copy the project binary to the 'bin' directory
+-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+\ No newline at end of file
++INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)