initPipeFrame: initialize the pipeFrame package

In wzthu/pipeFrame: Pipeline framework for bioinformatics in R

Description

This function should be called first in R terminal for general users. And it should be used in .onLoad() function for package developers. In this function, several parameters need to be defined and configured, including genome, job name, reference directory, temporary directory, check and install function, threads number, reference list, etc.

Usage

initPipeFrame(
  defaultJobName,
  availableGenome = c("hg19", "hg38", "mm9", "mm10", "danRer10", "galGal5", "galGal4",
    "rheMac3", "rheMac8", "panTro4", "rn5", "rn6", "sacCer2", "sacCer3", "susScr3",
    "testgenome"),
  defaultCheckAndInstallFunc = NULL,
  defaultThreads = 2,
  defaultTmpDir = getwd(),
  defaultRefDir = file.path(getwd(), "refdir"),
  defaultReference = list(test = list(file = "fileName", rc = "obj"))
)

Arguments

defaultJobName	Character scalar. The default job name for the package. When users use pipeFrame package, defaultJobName is "pipeFrame-pipeline".
availableGenome	Character scalar or vector. Configure the available valid genome such as "hg19", "mm10", etc.
defaultCheckAndInstallFunc	Function scalar. The function needs to call runWithFinishCheck
defaultThreads	Numeric scalar. The maximum thread limit for each step. Default:2
defaultTmpDir	Character scalar. The directory of intermediate results for all steps. Default: Current working directory.
defaultRefDir	Character scalar. The directory of reference data. Default: file.path(getwd(),"refdir")
defaultReference	List scalar. List of reference files.

Value

No value will be returned.

Examples

initPipeFrame(availableGenome = c("hg19", "hg38", "mm9", "mm10"),
              defaultJobName = paste0("pkgname","-pipeline")
)

wzthu/pipeFrame documentation built on Sept. 22, 2021, 4:36 p.m.