PrepareEnv: This function prepares the SCP Python environment by...

In zh542370159/SCP: Single Cell Pipeline

This function prepares the SCP Python environment by installing the required dependencies and setting up the environment.

Description

This function prepares the SCP Python environment by installing the required dependencies and setting up the environment.

Usage

PrepareEnv(
  conda = "auto",
  miniconda_repo = "https://repo.anaconda.com/miniconda",
  envname = NULL,
  version = "3.8-1",
  force = FALSE,
  ...
)

Arguments

conda	The path to a conda executable. Use "auto" to allow SCP to automatically find an appropriate conda binary.
miniconda_repo	Repositories for miniconda. Default is https://repo.anaconda.com/miniconda
envname	The name of a conda environment.
version	A character vector specifying the version of the environment (default is "3.8-1").
force	Whether to force a new environment to be created. If TRUE, the existing environment will be recreated. Default is FALSE
...	Other arguments passed to conda_install

Details

This function prepares the SCP Python environment by checking if conda is installed, creating a new conda environment if needed, installing the required packages, and setting up the Python environment for use with SCP. In order to create the environment, this function requires the path to the conda binary. If conda is set to "auto", it will attempt to automatically find the conda binary. If a conda environment with the specified name already exists and force is set to FALSE, the function will use the existing environment. If force set to TRUE, the existing environment will be recreated. Note that recreating the environment will remove any existing data in the environment. The function also checks if the package versions in the environment meet the requirements specified by the version parameter. The default is 3.8-1.

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.