Merge pull request easybuilders#19489 from boegel/20240104140049_new_…

…pr_dorado051

{bio}[foss/2022a] dorado v0.5.1 w/ CUDA 11.7.0

easybuild/easyconfigs/d/dorado/dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb

@@ -0,0 +1,74 @@
+easyblock = 'CMakeMake'
+
+name = 'dorado'
+version = '0.5.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/dorado'
+description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+# -Wno-error option is required to fix:
+# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used
+toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function"}
+
+source_urls = ['https://github.com/nanoporetech/dorado/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/nanoporetech',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = [None]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.12.2'),
+    ('zstd', '1.5.2'),
+    ('HTSlib', '1.15.1'),
+    ('kineto', '0.4.0'),
+    ('libaec', '1.0.6'),
+]
+
+# 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=$EBROOTOPENSSL && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# don't use vendored HTSlib, use provided HTSlib dependency
+preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
+# link with -lhts, not -lhtslib
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
+configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$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" '
+
+sanity_check_paths = {
+    'files': ['bin/dorado'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["dorado basecaller --help"]
+
+moduleclass = 'bio'