File: use_debian_packaged_gatb-core.patch

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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
Description: Use cmake input file of Debian packaged gatb-core

--- discosnp.orig/CMakeLists.txt
+++ discosnp/CMakeLists.txt
@@ -32,8 +32,8 @@
 ################################################################################
 # Define cmake modules directory
 ################################################################################
-SET (GATB_CORE_HOME  ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core)
-SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake)
+include(GNUInstallDirs)
+SET (CMAKE_MODULE_PATH /usr/${CMAKE_INSTALL_LIBDIR}/cmake)
 
 ################################################################################
 # THIRD PARTIES
@@ -43,9 +43,6 @@
 SET (GATB_CORE_EXCLUDE_TESTS     1)
 SET (GATB_CORE_EXCLUDE_EXAMPLES  1)
 
-# GATB CORE
-include (GatbCore)
-
 ################################################################################
 #  TOOLS GENERATION
 ################################################################################
--- discosnp.orig/tools/QHC/CMakeLists.txt
+++ discosnp/tools/QHC/CMakeLists.txt
@@ -16,13 +16,15 @@
 file (GLOB_RECURSE  ProjectFiles  src/*)
 
 # we define the artifact to be built: the project binary
+include(GNUInstallDirs)
+LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
 add_executable        (${PROJECT_NAME}  ${ProjectFiles})
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIRZ})
 
 
 # we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5 z )
 
 
 # We copy the project binary to the 'bin' directory
--- discosnp.orig/tools/kissnp2/CMakeLists.txt
+++ discosnp/tools/kissnp2/CMakeLists.txt
@@ -16,14 +16,16 @@
 file (GLOB_RECURSE  ProjectFiles  src/*)
 
 # we define the artifact to be built: the project binary
+include(GNUInstallDirs)
+LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
 add_executable        (${PROJECT_NAME}  ${ProjectFiles})
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIRZ})
 
 
 # we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5 z )
 
 
 # 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)
--- discosnp.orig/tools/kissreads2/CMakeLists.txt
+++ discosnp/tools/kissreads2/CMakeLists.txt
@@ -16,14 +16,16 @@
 file (GLOB_RECURSE  ProjectFiles  src/*)
 
 # we define the artifact to be built: the project binary
+include(GNUInstallDirs)
+LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
 add_executable        (${PROJECT_NAME}  ${ProjectFiles})
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIRZ})
 
 
 # we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5 z )
 
 
 # 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)
--- discosnp.orig/tools/read_file_names/CMakeLists.txt
+++ discosnp/tools/read_file_names/CMakeLists.txt
@@ -16,14 +16,16 @@
 file (GLOB_RECURSE  ProjectFiles  src/*)
 
 # we define the artifact to be built: the project binary
+include(GNUInstallDirs)
+LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
 add_executable        (${PROJECT_NAME}  ${ProjectFiles})
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIRZ})
 
 
 # we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5 z )
 
 
 # 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)
--- discosnp.orig/tools/create_coverage_h5_file/CMakeLists.txt
+++ discosnp/tools/create_coverage_h5_file/CMakeLists.txt
@@ -16,14 +16,16 @@
 file (GLOB_RECURSE  ProjectFiles  src/*)
 
 # we define the artifact to be built: the project binary
+include(GNUInstallDirs)
+LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
 add_executable        (${PROJECT_NAME}  ${ProjectFiles})
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIRZ})
 
 
 # we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME}  ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5 z )
 
 
 # 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)