basilisk.R

# scvelo 0.2.2 and latest version of dependencies in zellkonverter::AnnDataDependencies() succesfully tested.
.scvelo_dependencies <- c("alabaster==0.7.12",
    "anndata==0.7.4",
    "Babel==2.8.0",
    "brotlipy==0.7.0",
    "certifi==2020.6.20",
    "cffi==1.14.1",
    "chardet==3.0.4",
    "colorama==0.4.3",
    "cryptography==3.1",
    "cycler==0.10.0",
    "decorator==4.4.2",
    "docutils==0.16",
    "h5py==2.10.0",
    "idna==2.10",
    "imagesize==1.2.0",
    "importlib-metadata==1.7.0",
    "Jinja2==2.11.2",
    "joblib==0.16.0",
    "kiwisolver==1.2.0",
    "llvmlite==0.34.0",
    "loompy==2.0.16",
    "MarkupSafe==1.1.1",
    "matplotlib==3.3.1",
    "mock==4.0.2",
    "natsort==7.0.1",
    "networkx==2.5",
    "numba==0.51.2",
    "numexpr==2.7.1",
    "numpy==1.19.1",
    "olefile==0.46",
    "packaging==20.4",
    "pandas==1.1.2",
    "patsy==0.5.1",
    "Pillow==7.2.0",
    "pip==20.2.3",
    "pycparser==2.20",
    "Pygments==2.7.0",
    "pyOpenSSL==19.1.0",
    "pyparsing==2.4.7",
    "PySocks==1.7.1",
    "python==3.8",
    "python-dateutil==2.8.1",
    "pytz==2020.1",
    "requests==2.24.0",
    "scanpy==1.6.0",
    "scikit-learn==0.23.2",
    "scipy==1.5.2",
    "scvelo==0.2.2",
    "seaborn==0.11.0",
    "setuptools-scm==4.1.2",
    "sinfo==0.3.1",
    "six==1.15.0",
    "snowballstemmer==2.0.0",
    "Sphinx==3.2.1",
    "sphinxcontrib-applehelp==1.0.2",
    "sphinxcontrib-devhelp==1.0.2",
    "sphinxcontrib-htmlhelp==1.0.3",
    "sphinxcontrib-jsmath==1.0.1",
    "sphinxcontrib-qthelp==1.0.3",
    "sphinxcontrib-serializinghtml==1.1.4",
    "statsmodels==0.12.0",
    "stdlib-list==0.6.0",
    "threadpoolctl==2.1.0",
    "toml==0.10.1",
    "tornado==6.0.4",
    "tqdm==4.49.0",
    "typing_extensions==3.10.0.0",
    "umap-learn==0.4.6",
    "urllib3==1.25.10",
    "wheel==0.35.1",
    "zipp==3.1.0")

#' @importFrom basilisk BasiliskEnvironment
#' @importFrom zellkonverter AnnDataDependencies
velo.env <- BasiliskEnvironment("env", "velociraptor",
    packages=.scvelo_dependencies, channels = c("bioconda", "conda-forge"))