sctkPythonInstallConda {singleCellTK} | R Documentation

## 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", "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)

[Package singleCellTK version 2.0.0 Index]