Create wrapper and wrapper launcher for Tredparse

launch_tredparse.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## launch_wrapper_tredparse.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to launch the wrapper for qsubing Tredparse script for STR detection
+## Usage : FIXME
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191103
+## last revision date : 20191103
+## Known bugs : None
+
+INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+OUTPUTDIR=/user1/gad/an1770de/Tools/Tredparse/"$(date +"%F_%H-%M-%S")"
+LOGFILE="$OUTPUTDIR/log.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="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh"
+else 
+    qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
+fi

wrapper_tredparse.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## wrapper_tredparse.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : a wrapper for qsubing Tredparse script for STR detection
+## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191103
+## last revision date : 20191103
+## Known bugs : None
+
+
+# Log file path option
+if [ -z "$LOGFILE" ]
+then
+    LOGFILE=tredparse.$(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 "$(date +"%F_%H-%M-%S"): END"
+    touch tredparse.failed
+    exit 1
+fi
+
+# Check if output prefix is specified
+if [ -z "$OUTPUTDIR" ]
+then
+    echo "Output directory is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch tredparse.failed
+    exit 1
+fi
+
+# Enable the virtualenv
+TREDPARSE="/work/gad/shared/bin/tredparse/Tredparse-20190901"
+. "$TREDPARSE/bin/activate"
+
+# Launch script command and check exit code
+echo "command : FIXME"
+"$TREDPARSE/bin/tred.py" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19
+
+tredparse_exitcode=$?
+
+echo "tredparse exit code : $tredparse_exitcode"
+if [ $tredparse_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch tredparse.failed
+    exit 1
+fi
+
+echo "$(date +"%F_%H-%M-%S"): END"