nixpkgs/pkgs/applications/science/biology/minia/no-bundle.patch

diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
index f48a70b..0e11ece 100644
--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty)
 #  DEPENDENCIES 
 ################################################################################
 # we must be sure that hdf5 is built and installed before building gatb-core
-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
 
 ################################################################################
 #  DOCUMENTATION GENERATION 
@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
     INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt  DESTINATION . OPTIONAL)
     INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE              DESTINATION . OPTIONAL)
     INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md      DESTINATION . OPTIONAL)
-    INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
 ENDIF()
 
 ################################################################################
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
index dfeee1c..d5553a2 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+++ b/thirdparty/gatb-core/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/system/api/config.hpp>
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
index 60be5d5..25ae75e 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+++ b/thirdparty/gatb-core/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>
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
index 6a71bb0..b9205df 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+++ b/thirdparty/gatb-core/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  {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
index c22b892..62e6586 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.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  {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
index c06aaab..e0befba 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+++ b/thirdparty/gatb-core/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    [];
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
index 9659874..0c79ff6 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+++ b/thirdparty/gatb-core/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  {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
index 3cb84f8..cd5d382 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+++ b/thirdparty/gatb-core/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      {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
index b8f6c79..a040832 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
@@ -28,7 +28,7 @@
 
 #include <gatb/system/api/ISmartPointer.hpp>
 #include <gatb/tools/storage/impl/Storage.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb      {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
index 2645abd..fad48c0 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+++ b/thirdparty/gatb-core/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      {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
index a92b729..66d552f 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
@@ -40,7 +40,7 @@
 #include <string>
 #include <vector>
 #include <stdarg.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 
 /********************************************************************************/
 namespace gatb      {
diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
index 29e0949..0565cc4 100644
--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
@@ -33,7 +33,7 @@
 #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
 #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
 #include <gatb/system/impl/System.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
 #include <sstream>
 
 /********************************************************************************/
diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
index 6e0b5c4..34aef28 100644
--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
@@ -1,54 +1,3 @@
-################################################################################
-#  HDF5 GENERATION 
-################################################################################
-
-#SET (HDF5_ENABLE_THREADSAFE       ON)
-#SET (H5_HAVE_THREADSAFE 1)
-
-##########  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()
-
-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
-	OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
-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()
-
 # include other smaller libraries (json, Boophf)
 
 add_custom_target (thirdparty_copy ALL)