R/reticulate_setup.R
sctkPythonInstallVirtualEnv.Rd
Install all Python packages used in the singleCellTK
package
using virtualenv_install
from package reticulate
. This
will create a new virtual environment with the name envname
if not already present.
sctkPythonInstallVirtualEnv(
envname = "sctk-reticulate",
packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama",
"bbknn", "anndata"),
selectEnvironment = TRUE,
python = NULL
)
Character. Name of the virtual environment to create.
Character Vector. List of packages to install.
Boolean. Run selectSCTKVirtualEnvironment
after installing all packages to select the virtual environment. Default TRUE.
The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.
None. Installation of virtual environment.
See virtualenv_create
for more information on creating a Conda environment.
See virtualenv_install
for more description of the installation parameters.
See https://rstudio.github.io/reticulate/ for more information on package reticulate
.
See selectSCTKVirtualEnvironment
for reloading the virtual environment if R is restarted without
going through the whole installation process again.
if (FALSE) {
sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
}