Change output directory and queue type for jobs on qsub

parent b38301db
...@@ -16,8 +16,8 @@ ...@@ -16,8 +16,8 @@
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/user1/gad/an1770de/Analyses/ExpansionHunter/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
LOGFILE="$OUTPUTDIR/$DATE.log" LOGFILE="$OUTPUTDIR/$DATE.log"
# Launch the script on local host with --local option and on SGE with qsub without the --local option # Launch the script on local host with --local option and on SGE with qsub without the --local option
...@@ -26,5 +26,6 @@ then ...@@ -26,5 +26,6 @@ then
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
else else
qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
fi fi
...@@ -14,10 +14,10 @@ ...@@ -14,10 +14,10 @@
## last revision date : 20191103 ## last revision date : 20191103
## Known bugs : None ## Known bugs : None
DATE="$(date +"%F_%H-%M-%S")"
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTDIR="/user1/gad/an1770de/Analyses/Tredparse/$DATE" DATE="$(date +"%F_%H-%M-%S")"
LOGFILE="$OUTPUTDIR/$DATE.log" OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$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 # 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 ] if [ $# -eq 1 ] && [ "x$1" = x--local ]
...@@ -25,5 +25,6 @@ then ...@@ -25,5 +25,6 @@ then
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
INPUTFILE="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh" INPUTFILE="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh"
else else
qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
fi fi
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