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try an environment using anaconda
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@kevinrue
kevinrue committed Aug 29, 2024
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222 changes: 82 additions & 140 deletions R/basilisk.R
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## Linux ----

.scvelo.dependencies.Linux <- list(
channels = c("conda-forge", "bioconda"),
channels = c("anaconda", "conda-forge", "bioconda"),
packages = c(
'_libgcc_mutex==0.1',
'_openmp_mutex==4.5',
'absl-py==2.1.0',
'anndata==0.10.8',
'aom==3.9.1',
'anndata==0.10.9',
'array-api-compat==1.8',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'blas==1.0',
'bottleneck==1.3.7',
'brotli==1.0.9',
'brotli-bin==1.0.9',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.7.4',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.7.4',
'cffi==1.17.0',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'c-ares==1.19.1',
'ca-certificates==2024.7.2',
'chex==0.1.5',
'click==8.1.7',
'colorama==0.4.6',
'contextlib2==21.6.0',
'contourpy==1.2.1',
'cycler==0.12.1',
'dav1d==1.2.1',
'contourpy==1.2.0',
'cycler==0.11.0',
'dm-tree==0.1.7',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.2',
'exceptiongroup==1.2.2',
'filelock==3.15.4',
'flax==0.9.0',
'fonttools==4.53.1',
'exceptiongroup==1.2.0',
'filelock==3.13.1',
'flax==0.6.1',
'fonttools==4.51.0',
'freetype==2.12.1',
'fsspec==2024.6.1',
'fsspec==2024.3.1',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'gmp==6.2.1',
'gmpy2==2.1.2',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.8',
'importlib-metadata==8.4.0',
'importlib_metadata==8.4.0',
'importlib_resources==6.4.4',
'jax==0.4.31',
'jaxlib==0.4.31',
'hdf5==1.12.1',
'jax==0.3.25',
'jaxlib==0.3.25',
'jinja2==3.1.4',
'joblib==1.4.2',
'keyutils==1.6.1',
'kiwisolver==1.4.5',
'krb5==1.21.3',
'lcms2==2.16',
'ld_impl_linux-64==2.40',
'jpeg==9e',
'kiwisolver==1.4.4',
'krb5==1.20.1',
'lcms2==2.12',
'ld_impl_linux-64==2.38',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.1.1',
'lerc==3.0',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libbrotlicommon==1.0.9',
'libbrotlidec==1.0.9',
'libbrotlienc==1.0.9',
'libcblas==3.9.0',
'libcurl==8.9.1',
'libdeflate==1.21',
'libedit==3.1.20191231',
'libcurl==7.88.1',
'libdeflate==1.17',
'libedit==3.1.20230828',
'libev==4.33',
'libexpat==2.6.2',
'libffi==3.4.2',
'libffi==3.4.4',
'libgcc==14.1.0',
'libgcc-ng==14.1.0',
'libgfortran==14.1.0',
'libgfortran-ng==14.1.0',
'libgfortran5==14.1.0',
'libgfortran-ng==11.2.0',
'libgfortran5==11.2.0',
'libgomp==14.1.0',
'libgrpc==1.62.2',
'libhwloc==2.11.1',
'libiconv==1.17',
'libjpeg-turbo==3.0.0',
'liblapack==3.9.0',
'libllvm14==14.0.6',
'libnghttp2==1.58.0',
'libnsl==2.0.1',
'libopenblas==0.3.27',
'libpng==1.6.43',
'libprotobuf==4.25.3',
'libre2-11==2023.09.01',
'libsqlite==3.46.0',
'libnghttp2==1.57.0',
'libopenblas==0.3.21',
'libpng==1.6.39',
'libprotobuf==3.20.3',
'libssh2==1.11.0',
'libstdcxx==14.1.0',
'libstdcxx-ng==14.1.0',
'libtiff==4.6.0',
'libtorch==2.4.0',
'libuuid==2.38.1',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxcrypt==4.4.36',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.4.0',
'lightning-utilities==0.11.6',
'libtiff==4.5.1',
'libuuid==1.41.5',
'libwebp-base==1.3.2',
'lightning-utilities==0.9.0',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'mdurl==0.1.2',
'markdown-it-py==2.2.0',
'markupsafe==2.1.3',
'matplotlib-base==3.8.4',
'mdurl==0.1.0',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpc==1.1.0',
'mpfr==4.0.2',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'msgpack-python==1.0.3',
'mudata==0.3.0',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'natsort==7.1.1',
'ncurses==6.4',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numexpr==2.8.7',
'numpy==1.26.4',
'numpy-base==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.2',
'numpyro==0.13.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.3.1',
'opt-einsum==3.3.0',
'openssl==3.0.14',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'optax==0.1.4',
'packaging==24.1',
'pandas==2.2.2',
'patsy==0.5.6',
'pillow==10.4.0',
'pip==24.2',
'protobuf==4.25.3',
'pthread-stubs==0.4',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pygments==2.15.1',
'pynndescent==0.5.10',
'pyparsing==3.0.9',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.9',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python-dateutil==2.9.0post0',
'python-tzdata==2023.3',
'python_abi==3.11',
'pytorch==2.4.0',
'pytorch-lightning==2.4.0',
'pytorch==2.3.0',
'pytorch-lightning==1.9.5',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'pyyaml==6.0.1',
'readline==8.2',
'requests==2.32.3',
'rich==13.7.1',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6',
'scvi-tools==0.20.3',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==72.2.0',
'setuptools==72.1.0',
'six==1.16.0',
'sleef==3.6.1',
'snappy==1.2.1',
'sparse==0.15.4',
'sqlite==3.45.3',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.12.0',
'tensorstore==0.1.62',
'sympy==1.12',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'tk==8.6.14',
'toolz==0.12.0',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.5',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tqdm==4.66.4',
'typing-extensions==4.11.0',
'typing_extensions==4.11.0',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.2',
'wheel==0.44.0',
'xarray==2024.7.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'umap-learn==0.5.3',
'unicodedata2==15.1.0',
'wheel==0.43.0',
'xz==5.4.6',
'yaml==0.2.5',
'zipp==3.20.1',
'zstandard==0.23.0',
'zstd==1.5.6'
'zlib==1.2.13',
'zstd==1.5.5'
)
)

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