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#!/bin/bash
#BSUB -J {{{JOBNAME}}} # name of the job
#BSUB -cwd {{{CWD}}} # the workding dir for each job, this is <flow_run_path>/uniqueid/tmp
#BSUB -o {{{STDOUT}}} # output is sent to logfile, stdout + stderr by default
#BSUB -e {{{STDERR}}} # output is sent to logfile, stdout + stderr by default
#BSUB -q {{{QUEUE}}} # Job queue
#BSUB -W {{{WALLTIME}}} # Walltime in hours (usually for LSF). Please consult your sysadmin.
#BSUB -M {{{MEMORY}}} # Memory requirements in Kbytes
#BSUB -n {{{CPU}}} # CPU reserved
#BSUB -R span[ptile={{{CPU}}}] # CPU reserved, all reserved on same node
#BSUB -R rusage[mem={{{MEMORY}}}] # memory reserved
#BSUB -r # make the jobs re-runnable
#BSUB {{{DEPENDENCY}}} # Don't remove dependency args come here
#BSUB {{{EXTRA_OPTS}}} # Any extra arguments passed onto queue()
## ------------------------------ n o t e s -------------------------##
## All variables specified above are replaced on the fly.
## Most of them come from the flow_definition file.
## This is a core component of how flowr interacts with the cluster.
## Please refer to the platform manual, before editing this file
## ------------------------------------------------------------------##
## --- DO NOT EDIT from below here---- ##
## following will always overwrite previous output file, if any. See https://github.com/sahilseth/flowr/issues/13
set +o noclobber
touch {{{TRIGGER}}}
echo 'BGN at' $(date)
##--- add some custom module commands
{{{MODULE_CMDS}}}
## --- command to run comes here (flow_mat)
{{{CMD}}}
exitstat=$?
echo 'END at' $(date)
echo ${exitstat} > {{{TRIGGER}}}
exit ${exitstat}