Change queue on SGE

parent e953228e
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
## last revision date : 20191102 ## last revision date : 20191102
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
...@@ -27,5 +27,5 @@ then ...@@ -27,5 +27,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh qsub -pe smp 1 -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
fi fi
...@@ -11,10 +11,10 @@ ...@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104 ## Creation Date : 20191104
## last revision date : 20191104 ## last revision date : 20191117
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
...@@ -27,5 +27,5 @@ then ...@@ -27,5 +27,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh
fi fi
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
## last revision date : 20191104 ## last revision date : 20191104
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/HipSTR/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/HipSTR/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename -s .bam "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename -s .bam "$INPUTFILE")_$DATE"
...@@ -28,5 +28,5 @@ then ...@@ -28,5 +28,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTFILE="$OUTPUTFILE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_hipstr.sh" INPUTFILE="$INPUTFILE" OUTPUTFILE="$OUTPUTFILE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_hipstr.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_hipstr.sh qsub -pe smp 2 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTFILE="$OUTPUTFILE",LOGFILE="$LOGFILE" wrapper_hipstr.sh
fi fi
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
## last revision date : 20191104 ## last revision date : 20191104
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
...@@ -27,5 +27,5 @@ then ...@@ -27,5 +27,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_lobstr.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_lobstr.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh
fi fi
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
## last revision date : 20191103 ## last revision date : 20191103
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE"
LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log" LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
...@@ -26,5 +26,5 @@ then ...@@ -26,5 +26,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh" INPUTFILE="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
fi fi
...@@ -50,9 +50,10 @@ echo "command : FIXME" ...@@ -50,9 +50,10 @@ echo "command : FIXME"
/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR \ /work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR \
--bams "$INPUTFILE" \ --bams "$INPUTFILE" \
--fasta /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \ --fasta /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed \
--str-vcf "$OUTPUTFILE" --str-vcf "$OUTPUTFILE"
# --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
hipstr_exitcode=$? hipstr_exitcode=$?
echo "hipstr exit code : $hipstr_exitcode" echo "hipstr exit code : $hipstr_exitcode"
......
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