install_CondaSysReqs {Herper}R Documentation

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

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")

[Package Herper version 1.2.0 Index]