update dorado to properly use openssl from EB and not install externa…

…l EB libraries into its own lib directory.

easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb

@@ -20,10 +20,15 @@ sources = [{
     },
     'filename': SOURCE_TAR_GZ,
 }]
-patches = ['dorado-0.7.3_include-fstream.patch']
+patches = [
+    '%(name)s-%(version)s_include-fstream.patch',
+    '%(name)s-%(version)s_dont_install_external_libraries.patch',
+]
+
 checksums = [
     None,
     'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530',
+    '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac',
 ]
 
 builddependencies = [
@@ -45,7 +50,6 @@ dependencies = [
 # don't link to OpenSSL static libraries
 # fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
 preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
-preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
 # link in the ssl and crypto libs, to fix:
 # undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
 preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
@@ -63,12 +67,17 @@ preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
 
-configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
-configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
-configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib "
-# add -pthread flag (in addition to -lpthread) to avoid linking error:
-# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '
+_copts = [
+    "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
+    "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc",
+    '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL',
+    "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
+    # add -pthread flag (in addition to -lpthread) to avoid linking error:
+    # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+]
+
+configopts = ' '.join(_copts)
 
 sanity_check_paths = {
     'files': ['bin/dorado'],

easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch

@@ -0,0 +1,54 @@
+Don't install external libraries in Dorado's lib directory.
+
+Åke Sandgren, 2024-09-02
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a84c7524..0791dda8 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+         else()
+             # bundle the libraries from the cuda toolkit
+             file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}")
+-            install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
++            #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
+         endif()
+     endforeach()
+
+@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+         RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES)
+         foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES)
+ 	    if(${HDF_LIB} MATCHES "hdf5")
+-                install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug)
++                #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug)
+             endif()
+         endforeach()
+         FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT})
+         RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES)
+         foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES)
+ 	    if(${HDF_LIB} MATCHES "hdf5")
+-                install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo)
++                #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo)
+             endif()
+         endforeach()
+     endif()
+@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+     find_library(SZ_DLL sz REQUIRED)
+     get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY)
+     file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*")
+-    install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs)
+
+     find_library(AEC_DLL aec REQUIRED)
+     get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY)
+     file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*")
+-    install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs)
+
+     # If zstd has been dynamically linked, add the .so to the package
+     get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY)
+     file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*")
+-    install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs)
+
+ elseif(WIN32)
+     file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll")