Add --local option to the wrapper launcher for ExpansionHunter

parent f6feb237
...@@ -18,8 +18,10 @@ INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam ...@@ -18,8 +18,10 @@ INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX=test OUTPUTPREFIX=test
LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log 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
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment