#! /bin/sh ### ASDP PIPELINE ### ## wrapper_transfer.sh ## Version : 0.0.1 ## Licence : FIXME ## Description : a wrapper for qsubing bam transfer for STR pipeline ## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh ## Output : FIXME ## Requirements : FIXME ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Creation Date : 20191208 ## last revision date : 20191208 ## Known bugs : None # Log file path option if [ -z "$LOGFILE" ] then LOGFILE=transfer.$(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 "$(date +"%F_%H-%M-%S"): END" touch transfer.failed exit 1 fi # Check if output directory is specified if [ -z "$OUTPUTDIR" ] then echo "Output directory is not specified" echo "$(date +"%F_%H-%M-%S"): END" touch transfer.failed exit 1 fi # Transfer and check exit code echo "command : rsync -aAX \ $INPUTFILE $(echo "$INPUTFILE" | sed 's/\.bam$/.bai/') \ $OUTPUTDIR" rsync -aAX \ "$INPUTFILE" "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" \ "$OUTPUTDIR" transfer_exitcode=$? echo "transfer exit code : $transfer_exitcode" if [ $transfer_exitcode != 0 ] then echo "$(date +"%F_%H-%M-%S"): END" touch transfer.failed exit 1 fi echo "$(date +"%F_%H-%M-%S"): END"