minia: init at 3.2.1
This commit is contained in:
Justin Bedo
parent
6741cff527
commit
2191912274
33
pkgs/applications/science/biology/minia/default.nix
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33
pkgs/applications/science/biology/minia/default.nix
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@ -0,0 +1,33 @@
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{ stdenv, fetchFromGitHub, cmake, hdf5, boost }:
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stdenv.mkDerivation rec {
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pname = "minia";
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version = "3.2.1";
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src = fetchFromGitHub {
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owner = "GATB";
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repo = "minia";
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rev = "v${version}";
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sha256 = "0bmfrywixaaql898l0ixsfkhxjf2hb08ssnqzlzacfizxdp46siq";
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fetchSubmodules = true;
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};
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patches = [ ./no-bundle.patch ];
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NIX_CFLAGS_COMPILE = [ "-Wformat" ];
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nativeBuildInputs = [ cmake ];
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buildInputs = [ hdf5 boost ];
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prePatch = ''
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rm -rf thirdparty/gatb-core/gatb-core/thirdparty/{hdf5,boost}
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'';
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meta = with stdenv.lib; {
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description = "Short read genome assembler";
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homepage = "https://github.com/GATB/minia";
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license = licenses.agpl3;
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maintainers = with maintainers; [ jbedo ];
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platforms = [ "x86_64-linux" ];
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};
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}
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222
pkgs/applications/science/biology/minia/no-bundle.patch
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222
pkgs/applications/science/biology/minia/no-bundle.patch
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@ -0,0 +1,222 @@
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diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
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index f48a70b..0e11ece 100644
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--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt
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+++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
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@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty)
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# DEPENDENCIES
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################################################################################
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# we must be sure that hdf5 is built and installed before building gatb-core
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-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
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################################################################################
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# DOCUMENTATION GENERATION
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@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
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INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL)
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INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL)
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INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL)
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- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
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ENDIF()
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################################################################################
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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
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index dfeee1c..d5553a2 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
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@@ -35,7 +35,7 @@
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#include <stdint.h>
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#include <algorithm>
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#include <iostream>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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#include <gatb/system/api/Exception.hpp>
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#include <gatb/system/api/config.hpp>
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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
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index 60be5d5..25ae75e 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
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@@ -33,7 +33,7 @@
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/********************************************************************************/
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#include <iostream>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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#include <gatb/system/api/types.hpp>
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#include <gatb/tools/misc/api/Abundance.hpp>
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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
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index 6a71bb0..b9205df 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
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@@ -31,7 +31,7 @@
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#include <iostream>
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#include <gatb/system/api/types.hpp>
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#include <gatb/tools/misc/api/Abundance.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index c22b892..62e6586 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
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@@ -31,7 +31,7 @@
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#include <iostream>
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#include <gatb/system/api/types.hpp>
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#include <gatb/tools/misc/api/Abundance.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index c06aaab..e0befba 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
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@@ -31,7 +31,7 @@
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#include <iostream>
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#include <gatb/system/api/types.hpp>
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#include <gatb/tools/misc/api/Abundance.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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extern const unsigned char revcomp_4NT[];
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extern const unsigned char comp_NT [];
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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
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index 9659874..0c79ff6 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
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@@ -31,7 +31,7 @@
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#include <iostream>
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#include <gatb/system/api/types.hpp>
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#include <gatb/tools/misc/api/Abundance.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index 3cb84f8..cd5d382 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
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@@ -31,7 +31,7 @@
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/********************************************************************************/
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#include <sys/types.h>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index b8f6c79..a040832 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
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@@ -28,7 +28,7 @@
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#include <gatb/system/api/ISmartPointer.hpp>
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#include <gatb/tools/storage/impl/Storage.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index 2645abd..fad48c0 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
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@@ -40,7 +40,7 @@
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#include <string>
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#include <vector>
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#include <stdarg.h>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index a92b729..66d552f 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
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@@ -40,7 +40,7 @@
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#include <string>
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#include <vector>
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#include <stdarg.h>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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/********************************************************************************/
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namespace gatb {
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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
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index 29e0949..0565cc4 100644
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--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
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+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
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@@ -33,7 +33,7 @@
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#include <gatb/tools/storage/impl/CollectionHDF5.hpp>
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#include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
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#include <gatb/system/impl/System.hpp>
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-#include <hdf5/hdf5.h>
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+#include <hdf5.h>
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#include <sstream>
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/********************************************************************************/
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diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
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index 6e0b5c4..34aef28 100644
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--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
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+++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
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@@ -1,54 +1,3 @@
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-################################################################################
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-# HDF5 GENERATION
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-################################################################################
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-
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-#SET (HDF5_ENABLE_THREADSAFE ON)
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-#SET (H5_HAVE_THREADSAFE 1)
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-
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-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ##########
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-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools")
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-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz")
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-
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-SET (HDF5_EXTERNALLY_CONFIGURED ON)
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-
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-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
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-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
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-SET (HDF5_INSTALL_BIN_DIR bin)
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-SET (HDF5_INSTALL_LIB_DIR lib)
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-
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-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
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-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
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-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
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-
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-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
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- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5")
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-ENDIF()
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-
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-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
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- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
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-ENDIF()
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-
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-# We don't want warnings from HDF5 compilation
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-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w")
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-add_definitions (${COMPILE_DEFINITIONS})
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-
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-# add HDF5 generation
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-ADD_SUBDIRECTORY (hdf5)
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-
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-# We add a custom target for copying header files.
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-add_custom_target (hdf5_postbuild ALL)
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-
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-# We build the output directory
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-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
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-
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-# We define all the header files to be copied
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-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
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-
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-# We copy each header file
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-foreach (header ${headerfiles})
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- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} )
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-endforeach()
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-
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# include other smaller libraries (json, Boophf)
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add_custom_target (thirdparty_copy ALL)
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@ -23587,6 +23587,10 @@ in
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migrate = callPackage ../applications/science/biology/migrate { };
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minia = callPackage ../applications/science/biology/minia {
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boost = boost159;
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};
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mirtk = callPackage ../development/libraries/science/biology/mirtk { };
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muscle = callPackage ../applications/science/biology/muscle { };
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