Create wrapper and wrapper launcher for LobSTR

launch_lobstr.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## launch_wrapper_lobstr.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to launch the wrapper for qsubing LobSTR 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="$(date +"%F_%H-%M-%S")"
+OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$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 "$0")/wrapper_lobstr.sh"
+else 
+    mkdir -p "$OUTPUTDIR"
+    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh
+fi

wrapper_lobstr.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## wrapper_lobstr.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : a wrapper for qsubing LobSTR 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_lobstr.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 "$LOGFILE" ]
+then
+    LOGFILE=lobstr.$(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 "$(date +"%F_%H-%M-%S"): END"
+    touch lobstr.failed
+    exit 1
+fi
+
+# Check if output prefix is specified
+if [ -z "$OUTPUTPREFIX" ]
+then
+    echo "Output prefix is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch lobstr.failed
+    exit 1
+fi
+
+# Launch script command and check exit code
+echo "command : FIXME"
+#FIXME
+echo "command : FIXME /work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR \
+    --bampair -f /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
+    --rg-lib /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
+    --rg-sample /archive/gad/shared/bam_new_genome_temp/dijen017.bam \
+    --index-prefix /work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ \
+    -o ~/test \
+    -v"
+
+/work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR \
+    --bampair -f "$INPUTFILE" \
+    --rg-lib "$INPUTFILE" \
+    --rg-sample "$INPUTFILE" \
+    --index-prefix /work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ \
+    -o "$OUTPUTPREFIX" \
+    -v 
+
+
+lobstr_exitcode=$?
+
+echo "lobstr exit code : $lobstr_exitcode"
+if [ $lobstr_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch lobstr.failed
+    exit 1
+fi
+
+echo "$(date +"%F_%H-%M-%S"): END"