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Commit 776de494 authored by Anne-Sophie Denommé-Pichon's avatar Anne-Sophie Denommé-Pichon
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Add --local option to the wrapper launcher for ExpansionHunter

parent f6feb237
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Showing with 7 additions and 5 deletions
launch_expansionhunter.sh
View file @ 776de494
......@@ -18,8 +18,10 @@ INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX=test
LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
# Launch the script on local host with --local option and on SGE with qsub without the --local option
if [ $# -eq 1 ] && [ "x$1" = x--local ]
then
INPUTFILE="$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
fi
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