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Anne-Sophie Denommé-Pichon
STR
Commits
1c9c216b
Commit
1c9c216b
authored
Nov 05, 2019
by
Anne-Sophie Denommé-Pichon
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Create wrapper and wrapper launcher for HipSTR
parent
3f43954a
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launch_hipstr.sh
launch_hipstr.sh
+32
-0
wrapper_hipstr.sh
wrapper_hipstr.sh
+66
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launch_hipstr.sh
0 → 100755
View file @
1c9c216b
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_hipstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing HipSTR script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191104
## Known bugs : None
INPUTFILE
=
/archive/gad/shared/bam_new_genome_temp/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/HipSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
-s
.bam
"
$INPUTFILE
"
)
_
$DATE
"
OUTPUTFILE
=
"
$OUTPUTPREFIX
.vcf.gz"
LOGFILE
=
"
$OUTPUTDIR
/
$DATE
.log"
# 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
mkdir
-p
"
$OUTPUTDIR
"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTFILE
=
"
$OUTPUTFILE
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_hipstr.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_hipstr.sh
fi
wrapper_hipstr.sh
0 → 100755
View file @
1c9c216b
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_hipstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing HipSTR script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_hipstr.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191104
## Known bugs : None
# Log file path option
if
[
-z
"
$LOGFILE
"
]
then
LOGFILE
=
hipstr.
$(
date
+
"%F_%H-%M-%S"
)
.log
fi
# Logging
exec
1>>
"
$LOGFILE
"
2>&1
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: START"
# Check if input file exists
if
[
!
-f
"
$INPUTFILE
"
]
then
echo
"Input file '
$INPUTFILE
' does not exist"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
hipstr.failed
exit
1
fi
# Check if output prefix is specified
if
[
-z
"
$OUTPUTFILE
"
]
then
echo
"Output file is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
hipstr.failed
exit
1
fi
# Launch script command and check exit code
echo
"command : FIXME"
/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR
\
--bams
"
$INPUTFILE
"
\
--fasta
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions
/work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
\
--str-vcf
"
$OUTPUTFILE
"
hipstr_exitcode
=
$?
echo
"hipstr exit code :
$hipstr_exitcode
"
if
[
$hipstr_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
hipstr.failed
exit
1
fi
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
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