Subject: use HDF5 lib in Debian
Description: use Debian libs instead of embedded one
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2014-08-18
Forwarded: no
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp
@@ -35,7 +35,7 @@
 #include <stdint.h>
 #include <algorithm>
 #include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 #include <gatb/system/api/Exception.hpp>
 #include <gatb/tools/math/NativeInt64.hpp>
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
@@ -40,7 +40,7 @@
 #include <string>
 #include <vector>
 #include <stdarg.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb      {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
@@ -32,7 +32,7 @@
 
 #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
 #include <gatb/system/impl/System.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 #include <typeinfo>
 
 /********************************************************************************/
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp
@@ -33,7 +33,7 @@
 /********************************************************************************/
 
 #include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 #include <gatb/system/api/types.hpp>
 #include <gatb/tools/misc/api/Abundance.hpp>
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp
@@ -31,7 +31,7 @@
 #include <iostream>
 #include <gatb/system/api/types.hpp>
 #include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb  {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp
@@ -31,7 +31,7 @@
 #include <iostream>
 #include <gatb/system/api/types.hpp>
 #include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 extern const unsigned char revcomp_4NT[];
 extern const unsigned char comp_NT    [];
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp
@@ -31,7 +31,7 @@
 #include <iostream>
 #include <gatb/system/api/types.hpp>
 #include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb  {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
@@ -27,7 +27,7 @@
 #define _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_
 
 #include <gatb/system/api/ISmartPointer.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb      {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
@@ -31,7 +31,7 @@
 /********************************************************************************/
 
 #include <sys/types.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb      {
--- a/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
+++ b/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
@@ -2,47 +2,6 @@
 #  HDF5 GENERATION 
 ################################################################################
 
-SET (HDF5_ENABLE_THREADSAFE       ON)
-
-##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
-SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
-#SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
-
-SET (HDF5_EXTERNALLY_CONFIGURED     ON)
-
-#SET (HDF5_INSTALL_BIN_DIR           ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
-#SET (HDF5_INSTALL_LIB_DIR           ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
-SET (HDF5_INSTALL_BIN_DIR           bin)
-SET (HDF5_INSTALL_LIB_DIR           lib)
-
-SET (HDF5_INSTALL_INCLUDE_DIR       ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
-SET (HDF5_INSTALL_DATA_DIR          ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
-SET (HDF5_INSTALL_CMAKE_DIR         ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
-
-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
-    SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
-ENDIF()
-
-# We don't want warnings from HDF5 compilation
-set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
-add_definitions (${COMPILE_DEFINITIONS})
-
-# add HDF5 generation
-ADD_SUBDIRECTORY (hdf5)
-
-# We add a custom target for copying header files.
-add_custom_target (hdf5_postbuild ALL)
-
-# We build the output directory
-add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
-
-# We define all the header files to be copied
-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
-
-# We copy each header file
-foreach (header ${headerfiles})
-  add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR}  )
-endforeach()
 
 ################################################################################
 #  EMPHF GENERATION 
@@ -82,7 +41,6 @@
 #  INSTALL 
 ################################################################################
 IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
-    INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include)
     IF (DEFINED WITH_MPHF)
         INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/emphf DESTINATION include)
     ENDIF()
--- a/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
+++ b/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
@@ -197,7 +197,7 @@
 #  DEPENDENCIES 
 ################################################################################
 # we must be sure that hdf5 is built and installed before building gatb-core
-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
+ADD_DEPENDENCIES (gatbcore-static hdf5)
 
 IF (DEFINED WITH_MPHF)
     ADD_DEPENDENCIES(gatbcore-static emphf_copyasis)
