{bio}[gompi/2022a] LoRDEC v0.9, GATB-Core v1.4.2

easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb

@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'GATB-Core'
+version = '1.4.2'
+
+homepage = 'https://gatb.inria.fr/software/gatb-core'
+description = """GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly
+ efficient algorithms to analyse NGS data sets"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/GATB/gatb-core/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch']
+checksums = [
+    {'v1.4.2.tar.gz': '824c84a3712973746b977a9d49923fd499021a894225231100eaad1a66e9742d'},
+    {'GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch':
+     '938ff686e1fc8170b8ef4a73c1c0af059eb3eb76a6251b44a3dfddf991e05c63'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('HDF5', '1.12.2'),
+]
+
+start_dir = 'gatb-core'
+
+preconfigopts = "rm -r %(start_dir)s/thirdparty/{boost,hdf5} && "
+
+sanity_check_paths = {
+    'files': ['bin/dbginfo', 'bin/leon', 'lib/libgatbcore.a'],
+    'dirs': ['include/gatb'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch

@@ -0,0 +1,232 @@
+don't use vendored boost/hdf5 from gatb-core/thirdparty
+author: Kenneth Hoste (HPC-UGent)
+diff -ru gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt gatb-core-1.4.2/gatb-core/CMakeLists.txt
+--- gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/CMakeLists.txt	2023-03-31 21:25:42.862864064 +0200
+@@ -209,7 +209,7 @@
+ set (gatb-core-includes ${PROJECT_BINARY_DIR}/include  ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src  ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc})
+
+ # We define the libraries used for linking binary based on gatb core
+-set (gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5-static ${gatb-core-extra-libraries})
++set (gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5 ${gatb-core-extra-libraries})
+
+ # We define the directory where to find cmake helpers
+ set (gatb-core-cmake  ${CMAKE_MODULE_PATH})
+@@ -252,12 +252,6 @@
+ ADD_SUBDIRECTORY(thirdparty)
+
+ ################################################################################
+-#  DEPENDENCIES 
+-################################################################################
+-# we must be sure that hdf5 is built and installed before building gatb-core
+-ADD_DEPENDENCIES (gatbcore-static hdf5-static hdf5_postbuild)
+-
+-################################################################################
+ #  DOCUMENTATION GENERATION 
+ ################################################################################
+ IF (EXISTS "${PROJECT_SOURCE_DIR}/doc")
+@@ -286,7 +280,6 @@
+     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()
+
+ ################################################################################
+--- gatb-core-1.4.2.orig/gatb-core/thirdparty/CMakeLists.txt	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/thirdparty/CMakeLists.txt	2023-03-31 14:39:11.999034862 +0200
+@@ -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)
+@@ -63,7 +12,6 @@
+ #  INSTALL 
+ ################################################################################
+ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+-    INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include)
+     INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/json DESTINATION include)
+     INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/BooPHF DESTINATION include)
+ ENDIF ()
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -31,7 +31,7 @@
+ /********************************************************************************/
+
+ #include <sys/types.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp	2023-03-31 10:40:57.007450212 +0200
+@@ -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 -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp	2023-03-31 10:40:57.007450212 +0200
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp	2023-03-31 10:40:57.008450252 +0200
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp	2023-03-31 10:40:57.008450252 +0200
+@@ -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>
+
+ /********************************************************************************/

easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb

@@ -0,0 +1,45 @@
+easyblock = 'MakeCp'
+
+name = 'LoRDEC'
+version = '0.9'
+
+homepage = 'https://www.lirmm.fr/~rivals/lordec'
+description = """Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly
+accurate short reads (e.g., Illumina)."""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/']
+sources = ['lordec-src_%(version)s.tar.bz2']
+patches = [
+    'LoRDEC-0.9_GATB.patch',
+    'LoRDEC-0.9_GraphVector.patch',
+]
+checksums = [
+    {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'},
+    {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'},
+    {'LoRDEC-0.9_GraphVector.patch': '8c42dda643f8e1f79ee7d4ea2e3d8904cb755dc44cb907ada35b1e2873605ae5'},
+]
+
+local_gatb_version = '1.4.2'
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('GATB-Core', local_gatb_version),
+]
+
+build_cmd_targets = 'lordec_%s' % ''.join(local_gatb_version.split('.'))
+
+buildopts = "AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no GATB=${EBROOTGATBMINCORE}"
+
+local_bins = ['lordec-%s' % x for x in ('build-SR-graph', 'correct', 'stat', 'trim', 'trim-split')]
+
+files_to_copy = [(local_bins, 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%s --help 2>&1 | grep 'using GATB v%s'" % (x, local_gatb_version) for x in local_bins]
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch

@@ -0,0 +1,13 @@
+don't hardcode path to include/gatb/gatb_core.hpp so we can use GATB-Core provided as dependency
+author: Kenneth Hoste (HPC-UGent)
+--- lordec-src_0.9/Makefile.orig	2023-03-31 09:54:40.838204432 +0200
++++ lordec-src_0.9/Makefile	2023-03-31 09:55:42.987061551 +0200
+@@ -63,7 +63,7 @@
+ $(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): boost_include/boost/graph/graph_traits.hpp
+ endif
+ # ANYWAY we need GATB (compiled and installed) to compile all the objects
+-$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): gatb_v$(GATBVERSION)$(SUFFIX)/include/gatb/gatb_core.hpp
++$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): $(GATB)/include/gatb/gatb_core.hpp
+
+ # get version from a file
+ VERSION := $(shell cat version.txt)