Create wrapper and wrapper launcher for HipSTR

launch_hipstr.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## launch_wrapper_hipstr.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to launch the wrapper for qsubing HipSTR 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="$(date +"%F_%H-%M-%S")"
+OUTPUTDIR="/work/gad/shared/analyse/STR/HipSTR/$DATE"
+OUTPUTPREFIX="$OUTPUTDIR/$(basename -s .bam "$INPUTFILE")_$DATE"
+OUTPUTFILE="$OUTPUTPREFIX.vcf.gz"
+LOGFILE="$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"
+    INPUTFILE="$INPUTFILE" OUTPUTFILE="$OUTPUTFILE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_hipstr.sh"
+else 
+    mkdir -p "$OUTPUTDIR"
+    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_hipstr.sh
+fi

wrapper_hipstr.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## wrapper_hipstr.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : a wrapper for qsubing HipSTR script for STR detection
+## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_hipstr.sh
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191104
+## last revision date : 20191104
+## Known bugs : None
+
+
+# Log file path option
+if [ -z "$LOGFILE" ]
+then
+    LOGFILE=hipstr.$(date +"%F_%H-%M-%S").log
+fi
+
+# Logging
+exec 1>> "$LOGFILE" 2>&1
+echo "$(date +"%F_%H-%M-%S"): START"
+
+
+# Check if input file exists
+if [ ! -f "$INPUTFILE" ]
+then
+    echo "Input file '$INPUTFILE' does not exist"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch hipstr.failed
+    exit 1
+fi
+
+# Check if output prefix is specified
+if [ -z "$OUTPUTFILE" ]
+then
+    echo "Output file is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch hipstr.failed
+    exit 1
+fi
+
+# Launch script command and check exit code
+echo "command : FIXME"
+
+/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR \
+    --bams "$INPUTFILE" \
+    --fasta /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
+    --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed \
+    --str-vcf "$OUTPUTFILE"
+
+hipstr_exitcode=$?
+
+echo "hipstr exit code : $hipstr_exitcode"
+if [ $hipstr_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch hipstr.failed
+    exit 1
+fi
+
+echo "$(date +"%F_%H-%M-%S"): END"