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

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

Install Conda requirements listed in the System Requirement field of description

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	Channels for miniconda (bioconda and conda-forge are defaults).
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 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

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

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