#! /bin/sh ### ASDP PIPELINE ### ## launch_wrapper_gangstr.sh ## Version : 0.0.1 ## Licence : FIXME ## Description : script to launch the wrapper for qsubing GangSTR script for STR detection ## Usage : FIXME ## Output : FIXME ## Requirements : FIXME ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Creation Date : 20191104 ## last revision date : 20191126 ## Known bugs : None INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam DATE="$(date +"%F_%H-%M-%S")" OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log" INSERTMEAN="359.4" INSERTDEV="80.1204" # Launch the script on local host with --local option and on SGE with qsub without the --local option if [ $# -eq 1 ] && [ "x$1" = x--local ] then mkdir -p "$OUTPUTDIR" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" INSERTMEAN="$INSERTMEAN" INSERTDEV="$INSERTDEV" "$(dirname "$0")/wrapper_gangstr.sh" else mkdir -p "$OUTPUTDIR" qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE",INSERTMEAN="$INSERTMEAN",INSERTDEV="$INSERTDEV" wrapper_gangstr.sh fi