runWithFinishCheck: Install dependent data or software with finishing check

In pipeFrame: Pipeline framework for bioinformatics in R

Description

Install dependent data or software with finishing check

Usage

runWithFinishCheck(func, refName, refFilePath = NULL, genome = NULL)

checkAndInstallBSgenome(refFilePath, genome = getGenome())

checkAndInstallOrgDb(refFilePath, genome = getGenome())

checkAndInstallTxDb(refFilePath, genome = getGenome())

checkAndInstallGenomeFa(refFilePath)

Arguments

func	Function scalar. The function with refFilePath argument (reference file directory). The returned value will be set as the reference object.
refName	Character scalar. Reference name for getRef, getRefFiles and getRefRc.
refFilePath	Character scalar. The reference file relative directory under the "refdir/genome/"
genome	Character scalar. The genome like "hg19". Default: getGenome()

Value

runWithFinishCheck	No value will be returned
checkAndInstallBSgenome	check if there is the BSgenome package installed for curent genome and install it if not. No value will be returned.
checkAndInstallOrgDb	check if there is the OrgDb package installed for curent genome and install it if not. No value will be returned.
checkAndInstallTxDb	check if there is the TxDb package installed for curent genome and install it if not. Nothing will be returned.
checkAndInstallGenomeFa	check if genome FASTA file exist and install if not. No value will be returned

Examples

checkAndInstall <- function(){
   runWithFinishCheck(func = checkAndInstallBSgenome,refName = "bsgenome")
   runWithFinishCheck(func = checkAndInstallGenomeFa,refName = "fasta",
   refFilePath = paste0(getGenome(),".fa"))
}
initPipeFrame(availableGenome = c("hg19", "hg38","mm9","mm10","testgenome"),
              defaultJobName = paste0("pkgname","-pipeline")
)

setGenome("hg19")

pipeFrame documentation built on Nov. 8, 2020, 5:51 p.m.