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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| easyblock = 'CMakeMake' | ||
|
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| name = 'dorado' | ||
| version = '0.7.0' | ||
| versionsuffix = '-CUDA-%(cudaver)s' | ||
|
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| homepage = 'https://github.com/nanoporetech/dorado' | ||
| description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2023a'} | ||
| toolchainopts = {'usempi': True} | ||
|
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| 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, | ||
| }] | ||
| patches = ['dorado-0.7.2_include-fstream.patch'] | ||
| checksums = [ | ||
| None, | ||
| 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', | ||
| ] | ||
|
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| builddependencies = [ | ||
| ('binutils', '2.40'), | ||
| ('CMake', '3.26.3'), | ||
| ] | ||
|
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| dependencies = [ | ||
| ('CUDA', '12.1.1', '', SYSTEM), | ||
| ('OpenSSL', '1.1', '', SYSTEM), | ||
| ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), | ||
| ('HDF5', '1.14.0'), | ||
| ('zstd', '1.5.5'), | ||
| ('HTSlib', '1.18'), | ||
| ('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=$EBROOTOPENSSL && " | ||
| # link in the ssl and crypto libs, to fix: | ||
| # undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' | ||
| preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " | ||
|
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||
| # don't use vendored HTSlib, use provided HTSlib dependency | ||
| preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " | ||
| preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " | ||
| preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " | ||
| preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " | ||
| # link with -lhts, not -lhtslib | ||
| preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " | ||
| preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " | ||
|
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||
| # disable treating warnings like errors by stripping out -Werror | ||
| # cfr. https://github.com/nanoporetech/dorado/issues/779 | ||
| preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " | ||
|
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| configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " | ||
| configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$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" ' | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/dorado'], | ||
| 'dirs': [], | ||
| } | ||
|
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| sanity_check_commands = ["dorado basecaller --help"] | ||
|
|
||
| moduleclass = 'bio' |
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Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| easyblock = 'CMakeMake' | ||
|
|
||
| name = 'dorado' | ||
| version = '0.7.2' | ||
| 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': '2023b'} | ||
| toolchainopts = {'usempi': True} | ||
|
|
||
| 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, | ||
| }] | ||
| patches = ['dorado-0.7.2_include-fstream.patch'] | ||
|
|
||
| builddependencies = [ | ||
| ('binutils', '2.40'), | ||
| ('CMake', '3.27.6'), | ||
| ] | ||
|
|
||
| dependencies = [ | ||
| ('CUDA', '12.1.1', '', SYSTEM), | ||
| # ('OpenSSL', '1.1', '', SYSTEM), | ||
| # ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), | ||
| # ('HDF5', '1.14.0'), | ||
| # ('zstd', '1.5.5'), | ||
| # ('HTSlib', '1.18'), | ||
| # ('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 && " | ||
|
|
||
| # disable treating warnings like errors by stripping out -Werror | ||
| # 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" ' | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['bin/dorado'], | ||
| 'dirs': [], | ||
| } | ||
|
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| sanity_check_commands = ["dorado basecaller --help"] | ||
|
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||
| moduleclass = 'bio' |