install_CondaTools {Herper}R Documentation

Install Conda requirements.

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")

[Package Herper version 1.0.2 Index]