/
job.analysis.sh.tmpl
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/
job.analysis.sh.tmpl
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#!/bin/sh
#job
#PBS -N runAnalysis-<TMPL_VAR NAME=conditionSetTimeStamp>-<TMPL_VAR NAME=iJob>
#user
#PBS -P <TMPL_VAR NAME=linuxUser>:<TMPL_VAR NAME=linuxUser>
#notification
#PBS -M <TMPL_VAR NAME=emailAddress>
#PBS -m a
#resources
#PBS -l walltime=48:00:00
#PBS -l nodes=1:ppn=16
#PBS -l mem=22gb
#PBS -l vmem=22gb
#log
#PBS -o <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/out.analysis-<TMPL_VAR NAME=iJob>.log
#PBS -e <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/err.analysis-<TMPL_VAR NAME=iJob>.log
#PBS -W umask=002
#schedule
#PBS -W depend=afterany<TMPL_VAR NAME=afterany>
#set environment
export MATLAB_PREFDIR=/tmp/emptydir
export MCR_CACHE_ROOT=/tmp/mcr_cache_$PBS_JOBID
mkdir -p $MCR_CACHE_ROOT
#setup
cd <TMPL_VAR NAME=baseDir>
#set permissions
sudo chown -R <TMPL_VAR NAME=linuxUser>:<TMPL_VAR NAME=linuxUser> <TMPL_VAR NAME=outDir>/singleGeneDeletions/
chmod -R 775 <TMPL_VAR NAME=outDir>/singleGeneDeletions/
#run analysis
<TMPL_IF NAME=firstStageAnalysis>
./run.sh <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/bin/runAnalysis \
<TMPL_VAR NAME=pathToRunTime> \
<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/matlab.analysis.log \
<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp> <TMPL_VAR NAME=iJob> <TMPL_VAR NAME=nFirstStageJobs>
</TMPL_IF>
#compile summary
./compileSummary.pl <TMPL_VAR NAME=simulationIdx> <TMPL_VAR NAME=conditionSetTimeStamp>
#set permissions
sudo chown -R <TMPL_VAR NAME=linuxUser>:<TMPL_VAR NAME=linuxUser> <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/
chmod -R 775 <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/
sudo chown -R <TMPL_VAR NAME=linuxUser>:<TMPL_VAR NAME=linuxUser> <TMPL_VAR NAME=outDir>/singleGeneDeletions/
chmod -R 775 <TMPL_VAR NAME=outDir>/singleGeneDeletions/
#mail results
<TMPL_IF NAME=firstStageAnalysis>
<TMPL_ELSE>
./mailSimulationsSummary.pl <TMPL_VAR NAME=simulationIdx> <TMPL_VAR NAME=conditionSetTimeStamp>
</TMPL_IF>
#cleanup
rm -rf $MCR_CACHE_ROOT/*
#resources
echo ""
echo "=============="
echo "=== status ==="
echo "=============="
qstat -f $PBS_JOBID
#status
if [[ -f "<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/err.analysis.log" ]]
then
exit 1
fi
exit 0