#
# This sets all of my global options
#
#
sge.setDefaultOptions <- function() {
# user variables, feel free to change for more info help(sge.options)
#if the cluster should be used or if it should be run locally.
options(sge.use.cluster="TRUE")
# default number of elements per split
options(sge.block.size=100)
#prefix for data files
options(sge.file.prefix="Rsge_data")
#path for qsub
options(sge.qsub="qsub")
#path for qstat
options(sge.qstat="qstat")
#path for qacct
options(sge.qacct="qacct")
#user options for sge
options(sge.user.options="-S /bin/bash")
#extension for result files
options(sge.ret.ext="sge.ret")
#should qacct be used to help determine job status
options(sge.use.qacct=FALSE)
#should the files be removed afterwards (data files and sge output files)
options(sge.remove.files=TRUE)
#logging levels, this will be replaced by something useful soon
options(sge.debug=FALSE)
options(sge.trace=TRUE)
# should we save the global environment by default.
options(sge.save.global=FALSE)
# global variables that should not be changed, or should be changed very carefully.
options(sge.qsub.options="-cwd")
options(sge.qsub.blocking="-sync y -t 1-")
options(sge.script="RunSgeJob")
options(sge.monitor.script="MonitorJob.sh")
}
sge.options <- function(...) {
options(...)
}
sge.getOption <- function(...) {
getOption(...)
}
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