install_CondaSysReqs: Install Conda requirements listed in the System Requirement...

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_CondaSysReqs(
  pkg,
  channels = NULL,
  env = NULL,
  pathToMiniConda = NULL,
  updateEnv = FALSE,
  SysReqsAsJSON = FALSE,
  SysReqsSep = ",",
  verbose = FALSE
)

Arguments

pkg	Package to install Conda System Requirements from.
channels	Additional channels for miniconda (bioconda defaults and conda-forge are included automatically)
env	Name of Conda environment to install tools into.
pathToMiniConda	NULL Path to miniconda installation
updateEnv	Update existing package's conda environment if already installed.
SysReqsAsJSON	Parse the SystemRequirements in JSON format (see Details). Default is TRUE.
SysReqsSep	Separator used in SystemRequirement field.
verbose	Print messages on progress (Default is FALSE).

Value

Nothing returned. Output written to file.

Author(s)

Thomas Carroll

Examples

testPkg <- system.file("extdata/HerperTestPkg", package = "Herper")
install.packages(testPkg, type = "source", repos = NULL)
condaDir <- file.path(tempdir(), "r-miniconda")
condaPaths <- install_CondaSysReqs("HerperTestPkg", 
    pathToMiniConda = condaDir, SysReqsAsJSON = FALSE)
system2(file.path(condaPaths$pathToEnvBin, "samtools"), args = "--help")

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