install_CondaTools: Install Conda requirements.

In Herper: The Herper package is a simple toolset to install and manage conda packages and environments from R

Description

Install Conda requirements

Usage

install_CondaTools(
  tools,
  env,
  channels = NULL,
  pathToMiniConda = NULL,
  updateEnv = FALSE,
  search = TRUE,
  verbose = FALSE
)

Arguments

tools	Vector of software to install using conda.
env	Name of Conda environment to install tools into.
channels	Additional channels for miniconda (bioconda defaults and conda-forge are included automatically)
pathToMiniConda	NULL Path to miniconda installation
updateEnv	Update existing package's conda environment if already installed.
search	Whether to search for the package name and version before installing. It is highly recommended this be set to TRUE as information about available versions or similar packages will be included in the output if the exact match is not found.
verbose	Print messages on progress (Default is FALSE)

Value

Nothing returned. Output written to file.

Author(s)

Thomas Carroll

Examples

condaDir <- file.path(tempdir(), "r-miniconda")
condaPaths <- install_CondaTools("salmon", "salmon", pathToMiniConda = condaDir)
system2(file.path(condaPaths$pathToEnvBin, "salmon"), args = "--help")

Herper documentation built on Feb. 28, 2021, 2:02 a.m.