Create a wrapper launcher for ExpansionHunter

parent ac7f9b9e
*~
*.bam
*.bai
\ No newline at end of file
*.bai
*.sh.o*
*.sh.po*
*.failed
#*#
\ No newline at end of file
......@@ -13,3 +13,13 @@
## Creation Date : 20191102
## last revision date : 20191102
## Known bugs : None
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="$LOGFILE" wrapper_expansionhunter.sh
......@@ -5,7 +5,7 @@
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing ExpansionHunter script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=/path/to/the/matrix/file>,OUTPUTDIR=</path/to/the/output/dir>,[BASENAME=analysis_basename],[TESTTYPE=et|qlf|lrt],[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_expansionhunter.sh
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_expansionhunter.sh
## Output : FIXME
## Requirements : FIXME
......@@ -29,7 +29,7 @@ echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exists
if [ ! -f "$INPUTFILE" ]
then
echo "Input file does not exist"
echo "Input file '$INPUTFILE' does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch expansionhunter.failed
exit 1
......@@ -46,21 +46,17 @@ fi
# Create .bam and .bai symbolic links
TMPDIR="$(mktemp -d)"
ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFLE")"
ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFILE")"
ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
#FIXME TODO create a pipeline to launch the qsub script
#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bam ./dijen017.bam
#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bai ./dijen017.bam.bai
# Launch script command and check exit code
echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
--reads "$TMPDIR/$(basename "$INPUTFLE")" \
--reads "$TMPDIR/$(basename "$INPUTFILE")" \
--reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
--output-prefix "$OUTPUTPREFIX""
--output-prefix $OUTPUTPREFIX"
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
--reads "$TMPDIR/$(basename "$INPUTFLE")" \
--reads "$TMPDIR/$(basename "$INPUTFILE")" \
--reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
--output-prefix "$OUTPUTPREFIX"
......@@ -81,8 +77,3 @@ then
fi
echo "$(date +"%F_%H-%M-%S"): END"
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