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Commit c7b5da6e authored by Anne-Sophie Denommé-Pichon's avatar Anne-Sophie Denommé-Pichon
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Handle ehdn outlier analyses on SGE for all patients

parent 35460f6a
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Showing with 3 additions and 3 deletions
launch_ehdn_outlier.sh 100644 → 100755
View file @ c7b5da6e
...@@ -13,10 +13,10 @@ ...@@ -13,10 +13,10 @@
## Last revision date: 20200215 ## Last revision date: 20200215
## Known bugs: None ## Known bugs: None
CASE=dijen001 CASE="$1"
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunterDeNovoOutlier/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunterDeNovoOutlier/$DATE"
LOGFILE="$OUTPUTDIR/$DATE.log" LOGFILE="$OUTPUTDIR/$DATE.$CASE.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$1" = x--local ]
...@@ -25,5 +25,5 @@ then ...@@ -25,5 +25,5 @@ then
CASE="$CASE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh" CASE="$CASE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q batch -v CASE="$CASE",LOGFILE="$LOGFILE" wrapper_ehdn_outlier.sh qsub -pe smp 1 -q batch -N "ehdn_outlier_$CASE" -sync y -v CASE="$CASE",LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
fi fi
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