added scAtomic

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rCASC
-Version: 5.5.8
-Date: 2024-05-17
+Version: 5.5.9
+Date: 2024-06-29
 Title: rCASC reproducible Classification Analysis of Single Cell Sequencing Data
 Authors@R: c(person("Raffaele", "Calogero", role = c("aut", "cre"),
                      email = "raffaele.calogero@unito.it"),

R/scAtomic.R

@@ -0,0 +1,118 @@
+ #' @title scAtomic
+#' @description This function executes a ubuntu docker that execute scAtomic on a csv file
+#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
+#' @param scratch.folder, a character string indicating the path of the scratch folder
+#' @param file, a character string indicating the path of the file, with file name and extension included
+#' @param separator, separator used in count file, e.g. '\\t', ','
+
+#' @author Raffaele Calogero
+#'
+#' @return results
+#'
+#' @examples
+#' \dontrun{
+#'scAtomic(group="docker",scratch.folder="/home/lucastormreig/sc-atomic/wtc1cls1/",file="/home/lucastormreig/sc-atomic/wtc1cls1/s1abr_wt_c1_Cluster1.csv",separator=",")
+#'}
+#' @export
+scAtomic <- function(group=c("sudo","docker"), scratch.folder, file, separator){
+
+data.folder=dirname(file)
+positions=length(strsplit(basename(file),"\\.")[[1]])
+matrixNameC=strsplit(basename(file),"\\.")[[1]]
+matrixName=paste(matrixNameC[seq(1,positions-1)],collapse="")
+format=strsplit(basename(basename(file)),"\\.")[[1]][positions]
+
+
+  #running time 1
+  ptm <- proc.time()
+  #setting the data.folder as working folder
+  if (!file.exists(data.folder)){
+    cat(paste("\nIt seems that the ",data.folder, " folder does not exist\n"))
+    return(2)
+  }
+
+  #storing the position of the home folder
+  home <- getwd()
+  setwd(data.folder)
+  #initialize status
+  system("echo 0 > ExitStatusFile 2>&1")
+
+  #testing if docker is running
+  test <- dockerTest()
+  if(!test){
+    cat("\nERROR: Docker seems not to be installed in your system\n")
+    system("echo 10 > ExitStatusFile 2>&1")
+    setwd(home)
+    return(10)
+  }
+
+
+
+  #check  if scratch folder exist
+  if (!file.exists(scratch.folder)){
+    cat(paste("\nIt seems that the ",scratch.folder, " folder does not exist\n"))
+    system("echo 3 > ExitStatusFile 2>&1")
+    setwd(data.folder)
+    return(3)
+  }
+  tmp.folder <- gsub(":","-",gsub(" ","-",date()))
+  scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
+  writeLines(scrat_tmp.folder,paste(data.folder,"/tempFolderID", sep=""))
+  cat("\ncreating a folder in scratch folder\n")
+  dir.create(file.path(scrat_tmp.folder))
+  #preprocess matrix and copying files
+
+if(separator=="\t"){
+separator="tab"
+}
+
+system(paste("cp ",data.folder,"/",matrixName,".",format," ",scrat_tmp.folder,"/",sep=""))
+
+
+  #executing the docker job
+    params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder, ":/data -d repbioinfo/scatomicr Rscript /home/command.R ",matrixName," ",format," ",separator,sep="")
+
+resultRun <- runDocker(group=group, params=params)
+
+  #waiting for the end of the container work
+  if(resultRun==0){
+    #system(paste("cp ", scrat_tmp.folder, "/* ", data.folder, sep=""))
+  }
+  #running time 2
+  ptm <- proc.time() - ptm
+  dir <- dir(data.folder)
+  dir <- dir[grep("run.info",dir)]
+  if(length(dir)>0){
+    con <- file("run.info", "r")
+    tmp.run <- readLines(con)
+    close(con)
+    tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
+    tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
+    tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
+    writeLines(tmp.run,"run.info")
+  }else{
+    tmp.run <- NULL
+    tmp.run[1] <- paste("run time mins ",ptm[1]/60, sep="")
+    tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
+    tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
+
+    writeLines(tmp.run,"run.info")
+  }
+
+  #saving log and removing docker container
+  container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
+  system(paste("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/", substr(container.id,1,12),".log", sep=""))
+  system(paste("docker rm ", container.id, sep=""))
+
+
+  #Copy result folder
+  cat("Copying Result Folder")
+  system(paste("cp -r ",scrat_tmp.folder,"/* ",data.folder,sep=""))
+  #removing temporary folder
+  cat("\n\nRemoving the temporary file ....\n")
+  system(paste("rm -R ",scrat_tmp.folder))
+  system("rm -fR out.info")
+  system("rm -fR dockerID")
+  system("rm  -fR tempFolderID")
+  setwd(home)
+}