Added Slurm support

CompEpigen · Nov 17, 2020 · f9b2a34 · f9b2a34
1 parent d13c1d5
commit f9b2a34
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/R/start_analysis.R b/R/start_analysis.R
@@ -231,7 +231,8 @@ start.refreeewas.analysis <- function(meth.data=NULL,
 #' @param cores Integer representing the number of cores to be used in the analysis.
 #' @param itermax Maximum number of iterations
 #' @param ninit Number if initialtions.
-#' @param cluster.submit Flag indicating, if the jobs are to be submitted to a scientific compute cluster (only SGE supported).
+#' @param cluster.submit Flag indicating, if the jobs are to be submitted to a scientific compute cluster (only SGE and SLURM supported).
+#' @param cluster.architecture The cluster architecture used. Currently \code{'SGE'} and \code{'SLURM'} supported
 #' @param cluster.R.dir Path to an executable version of R.
 #' @param cluster.hostlist Regular expression, on which basis hosts are selected in the cluster environment.
 #' @param cluster.memlimit the \code{memlimit} resource value of the cluster submission.
@@ -265,6 +266,7 @@ start.medecom.analysis<-function(
  itermax=1000,
  ninit=100,
  cluster.submit=FALSE,
+ cluster.architecture="SGE",
  cluster.R.dir=NA,
  cluster.hostlist="*",
  cluster.memlimit="5G",
@@ -358,7 +360,7 @@ start.medecom.analysis<-function(
  }
  }
  if(cluster.submit){
- cluster.settings=list(R_bin_dir=cluster.R.dir, host_pattern=cluster.hostlist, mem_limit=cluster.memlimit)
+ cluster.settings=list(R_bin_dir=cluster.R.dir, host_pattern=cluster.hostlist, mem_limit=cluster.memlimit,cluster_architecture=cluster.architecture)
  }else{
  cluster.settings=NULL
  }
@@ -531,7 +533,8 @@ start.medecom.analysis<-function(
 #' @param cores Integer representing the number of cores to be used in the analysis.
 #' @param itermax Maximum number of iterations
 #' @param ninit Number if initialtions.
-#' @param cluster.submit Flag indicating, if the jobs are to be submitted to a scientific compute cluster (only SGE supported).
+#' @param cluster.submit Flag indicating, if the jobs are to be submitted to a scientific compute cluster (only SGE and SLURM supported).
+#' @param cluster.architecture The cluster architecture used. Currently \code{'SGE'} and \code{'SLURM'} supported
 #' @param cluster.Rdir Path to an executable version of R.
 #' @param cluster.hostlist Regular expression, on which basis hosts are selected in the cluster environment.
 #' @param cluster.memlimit the \code{memlimit} resource value of the cluster submission.
@@ -598,6 +601,7 @@ start.decomp.pipeline <- function(rnb.set,
  itermax=1000,
  ninit=100,
  cluster.submit=FALSE,
+ cluster.architecture="SGE",
  cluster.Rdir=NA,
  cluster.hostlist="*",
  cluster.memlimit="5G",
@@ -705,6 +709,7 @@ start.decomp.pipeline <- function(rnb.set,
  itermax=itermax,
  ninit=ninit,
  cluster.submit=cluster.submit,
+ cluster.architecture=cluster.architecture,
  cluster.R.dir=cluster.Rdir,
  cluster.hostlist=cluster.hostlist,
  cluster.memlimit=cluster.memlimit,