sctkPythonInstallConda: Installs Python packages into a Conda environment

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Installs Python packages into a Conda environment

Description

Install all Python packages used in the singleCellTK package using conda_install from package reticulate. This will create a new Conda environment with the name envname if not already present. Note that Anaconda or Miniconda already need to be installed on the local system.

Usage

sctkPythonInstallConda(
  envname = "sctk-reticulate",
  conda = "auto",
  packages = c("scipy", "numpy", "astroid", "six"),
  pipPackages = c("scrublet", "scanpy", "louvain", "leidenalg", "bbknn", "scanorama",
    "anndata"),
  selectConda = TRUE,
  forge = FALSE,
  pipIgnoreInstalled = TRUE,
  pythonVersion = NULL,
  ...
)

Arguments

envname	Character. Name of the conda environment to create.
conda	Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.
packages	Character Vector. List of packages to install from Conda.
pipPackages	Character Vector. List of packages to install into the Conda environment using 'pip'.
selectConda	Boolean. Run selectSCTKConda after installing all packages to select the Conda environment. Default TRUE.
forge	Boolean. Include the Conda Forge repository.
pipIgnoreInstalled	Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades. The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult to install via pip due to compilation requirements).
pythonVersion	Passed to python_version variable in conda_install. Default NULL.
...	Other parameters to pass to conda_install.

Value

None. Installation of Conda environment.

See Also

See conda_create for more information on creating a Conda environment. See conda_install for more description of the installation parameters. See https://rstudio.github.io/reticulate/ for more information on package reticulate. See selectSCTKConda for reloading the Conda environment if R is restarted without going through the whole installation process again. See https://docs.conda.io/en/latest/ for more information on Conda environments.

Examples

## Not run: 
sctkPythonInstallConda(envname = "sctk-reticulate")

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.