R/onLoad.R

In pipeFrame: Pipeline framework for bioinformatics in R

#' @rdname initPipeFrame
#' @title initialize the pipeFrame package
#' @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.
#' @param defaultJobName \code{Character} scalar.
#' The default job name for the package. When users use pipeFrame package,
#' defaultJobName is "pipeFrame-pipeline".
#' @param availableGenome \code{Character} scalar or vector.
#' Configure the available valid genome such as "hg19", "mm10", etc.
#' @param defaultCheckAndInstallFunc \code{Function} scalar.
#' The function needs to call  \code{\link{runWithFinishCheck}}
#' @param defaultThreads \code{Numeric} scalar.
#' The maximum thread limit for each step. Default:2
#' @param defaultTmpDir \code{Character} scalar.
#' The directory of intermediate results for all steps.
#' Default: Current working directory.
#' @param defaultRefDir \code{Character} scalar.
#' The directory of reference data.
#' Default: \code{file.path(getwd(),"refdir")}
#' @param defaultReference \code{List} scalar. List of reference files.
#' @return No value will be returned.
#' @examples
#' initPipeFrame(availableGenome = c("hg19", "hg38", "mm9", "mm10"),
#'               defaultJobName = paste0("pkgname","-pipeline")
#' )
#'
#' @export
initPipeFrame <- function(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"),
                          #file.path("~",".pipeFrame","refdir"),
                          defaultReference = list(
                              test=list(file="fileName",rc = "obj"))
){
    allvalidgenome <- c("hg19",
                        "hg38",
                        "mm9",
                        "mm10",
                        "danRer10",
                        "galGal5",
                        "galGal4",
                        "rheMac3",
                        "rheMac8",
                        "panTro4",
                        "rn5",
                        "rn6",
                        "sacCer2",
                        "sacCer3",
                        "susScr3",
                        "testgenome")

    if(defaultJobName == "pipeFrame-pipeline"){
        oldavailgenome <- allvalidgenome
    }else{
        oldavailgenome <- getOption("pipeFrameConfig.genome.valid")
    }

    options(pipeFrameConfig.threads = defaultThreads)
    if(!is.null(availableGenome) && !is.null(oldavailgenome)){
        notvalid <- setdiff(availableGenome,allvalidgenome)
        if(length(notvalid) > 0){
            stop(paste(paste(notvalid,collapse = ","),"is not available for pipeFrame"))
        }
        options(pipeFrameConfig.genome.valid =
                    intersect(availableGenome,oldavailgenome))
    }else{
        options(pipeFrameConfig.genome.valid = NULL)
    }
    allowChange = getOption("pipeFrameConfig.allowChangeJobDir")
    if(is.null(allowChange)){
        allowChange <- TRUE
        options(pipeFrameConfig.allowChangeJobDir = TRUE)
    }
    if(allowChange){
        tryCatch({if(getJobName()=="pipeFrame-pipeline"){
            setJobName(defaultJobName)
        }},
        error = function(cond){
            setJobName(defaultJobName)
        })
        tryCatch(getTmpDir(),
                 error = function(cond){
                     setTmpDir(defaultTmpDir)
                 })
    }
    tryCatch(getRefDir(),
             error = function(cond){
                 if(!file.exists("DESCRIPTION")){
                     setRefDir(defaultRefDir)
                 }
             })
    cni<-getOption("pipeFrameConfig.genome.checkAndInstallFunc")
    if(is.null(defaultCheckAndInstallFunc)){
        options(pipeFrameConfig.genome.checkAndInstallFunc =
                    c(cni,checkAndInstall))
    }else{
        #       print(defaultCheckAndInstallFunc)
        #       stopifnot(!is.function(defaultCheckAndInstallFunc))
        options(pipeFrameConfig.genome.checkAndInstallFunc =
                    c(cni,defaultCheckAndInstallFunc))
    }

    options(pipeFrameConfig.genome.refs = defaultReference)

    count <- getOption("pipeFrameConfig.count")
    if(is.null(count)){
        options(pipeFrameConfig.count = 0L)
    }

    options(pipeFrameConfig.nameObjList = list())
    options(pipeFrameConfig.ignoreCheck = FALSE)


}

.onLoad <- function(libname, pkgname) {
    initPipeFrame(defaultJobName = paste0(pkgname,"-pipeline"))
}