runWithFinishCheck {pipeFrame} | R Documentation |
Install dependent data or software with finishing check
runWithFinishCheck(func, refName, refFilePath = NULL) checkAndInstallBSgenome(refFilePath, genome = getGenome()) checkAndInstallOrgDb(refFilePath, genome = getGenome()) checkAndInstallTxDb(refFilePath, genome = getGenome()) checkAndInstallGenomeFa(refFilePath)
func |
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refName |
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refFilePath |
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genome |
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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 |
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")