Change local output directory and add time stamp in log file names

parent 7264b1f2
......@@ -15,12 +15,15 @@
## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/"$(date +"%F_%H-%M-%S")"
LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/user1/gad/an1770de/Analyses/ExpansionHunter/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$DATE"
LOGFILE="$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="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
else
qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
......
......@@ -14,9 +14,10 @@
## last revision date : 20191103
## Known bugs : None
DATE="$(date +"%F_%H-%M-%S")"
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTDIR=/user1/gad/an1770de/Tools/Tredparse/"$(date +"%F_%H-%M-%S")"
LOGFILE="$OUTPUTDIR/log.log"
OUTPUTDIR="/user1/gad/an1770de/Analyses/Tredparse/$DATE"
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 ]
......
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