Create script to launch EHDN outlier analyses on SGE

launch_ehdn_outlier.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## Version: 0.0.1
+## Licence: FIXME
+## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
+## Usage: FIXME
+## Output: FIXME
+## Requirements: FIXME
+
+## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date: 20200215
+## Last revision date: 20200215
+## Known bugs: None
+
+CASE=dijen001
+DATE="$(date +"%F_%H-%M-%S")"
+OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunterDeNovoOutlier/$DATE"
+LOGFILE="$OUTPUTDIR/$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"
+    CASE="$CASE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
+else 
+    mkdir -p "$OUTPUTDIR"
+    qsub -pe smp 1 -q batch -v CASE="$CASE",LOGFILE="$LOGFILE" wrapper_ehdn_outlier.sh
+fi