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#! /bin/sh
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## 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
# Source the configuration file
. "$(dirname "$0")/config.sh"
# Log file path option
if [ -z "$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"
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"
exit 1
fi
# Enable the virtualenv if any
if [ -n "$TREDPARSE_VENV" ]
then
. "$TREDPARSE_VENV"
fi
# Launch script command and check exit code
echo "command : $TREDPARSE $INPUTFILE --workdir $OUTPUTDIR --ref hg19"
"$TREDPARSE" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19
tredparse_exitcode=$?
echo "tredparse exit code : $tredparse_exitcode"
if [ $tredparse_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"