install_CondaTools: Install Conda requirements.

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

Install Conda requirements.

Description

Install Conda requirements

Usage

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

Arguments

tools	Vector of software to install using conda.
env	Name of Conda environment to install tools into.
channels	Channels for miniconda (bioconda and conda-forge are defaults).
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 system messages from conda on progress (Default is FALSE). There is a third option "silent" which suppresses Herper and Conda messaging.

Value

Nothing returned. Output written to file.

Author(s)

Thomas Carroll

Examples

condaPaths <- install_CondaTools("salmon", "herper_env")
system2(file.path(condaPaths$pathToEnvBin, "salmon"), args = "--help")

RockefellerUniversity/Herper documentation built on Feb. 19, 2024, 7:29 p.m.