#' makeBranch
#'
#' @param branchName
#' @param pipelineStep
#' @param configFile
#' @param infoTsv
#'
#' @return
#' @keywords internal
#'
#' @examples
makeBranch<-function(branchName, pipelineStep, configFile="./HCR.config", infoTsv){
#pipelineStep possibility: Binning, Downstream, Filtering, Normalization,
# Pre-Processing, Report, Visualization
workingDir<-paste0(getwd(),as.character((read.table(configFile))[1,1]))
it<-as.matrix(data.frame(read.table(infoTsv, sep="\t")))
if (length(it[1,]==3)){
it<-it[,-1]
}
mainPrj<-it[4,2]
mainPath<-paste0(workingDir,"HiCeekRwd/Projects/",mainPrj,"/")
currentProject<-it[5,2]
it[5,2]<-branchName
pipStep<-c("Pre-Processing", "Filtering", "Binning",
"Normalization", "Downstream", "Report")
# itNames<-c("InputPath", "Resolution", "Type",
# "ProjectName", "AnalysisName","comment")
# itValues<-c(shinyFilesPath(input$bamFile) , input$binSize,
# input$inputType, prjName, input$anNewName,
# paste0("Reference Genome:",
# shinyFilesPath(input$refGenome, last=TRUE)))
if (dir.exists(paste0(mainPath,branchName))==FALSE){
makeHCRan(branchName, mainPath, infoTable=it)
file.copy(paste0(mainPath,currentProject), paste0(mainPath,branchName))
for (i in 1:(which(pipStep==pipelineStep)-1)){
print (paste0("i:",i))
print(paste0("mainPath:",mainPath,
" branchName:",branchName,
" currentProject:",currentProject))
sysFiles<-list.files(paste0(mainPath,currentProject), recursive=TRUE)
#print(sysFiles)
sysFiles<-sysFiles[grep(paste0("/", pipStep[i]) ,sysFiles, fixed=TRUE)]
#print(sysFiles)
if (length(sysFiles)>=1){
for (j in 1:length(sysFiles)){
print (paste0("j:",j))
file.copy(paste0(mainPath,currentProject,"/",sysFiles[j]),
paste0(mainPath,branchName,"/",sysFiles[j]),
overwrite=TRUE)
}
}
}
} else {
return(print("already existing folder"))
}
}
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