Create script to launch GangSTR wrapper

launch_gangstr.sh

+#! /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 : 20191104
+## Known bugs : None
+
+INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.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"
+
+# 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="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh"
+else 
+    mkdir -p "$OUTPUTDIR"
+    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh
+fi