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Anne-Sophie Denommé-Pichon
STR
Commits
3f43954a
Commit
3f43954a
authored
Nov 04, 2019
by
Anne-Sophie Denommé-Pichon
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Create wrapper and wrapper launcher for LobSTR
parent
7a5daf35
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launch_lobstr.sh
launch_lobstr.sh
+31
-0
wrapper_lobstr.sh
wrapper_lobstr.sh
+77
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launch_lobstr.sh
0 → 100755
View file @
3f43954a
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_lobstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing LobSTR 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/LobSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$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
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_lobstr.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_lobstr.sh
fi
wrapper_lobstr.sh
0 → 100755
View file @
3f43954a
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_lobstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing LobSTR 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_lobstr.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
=
lobstr.
$(
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
lobstr.failed
exit
1
fi
# Check if output prefix is specified
if
[
-z
"
$OUTPUTPREFIX
"
]
then
echo
"Output prefix is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
lobstr.failed
exit
1
fi
# Launch script command and check exit code
echo
"command : FIXME"
#FIXME
echo
"command : FIXME /work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR
\
--bampair -f /archive/gad/shared/bam_new_genome_temp/dijen017.bam
\
--rg-lib /archive/gad/shared/bam_new_genome_temp/dijen017.bam
\
--rg-sample /archive/gad/shared/bam_new_genome_temp/dijen017.bam
\
--index-prefix /work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_
\
-o ~/test
\
-v"
/work/gad/shared/bin/lobstr/lobSTR-4.0.6/bin/lobSTR
\
--bampair
-f
"
$INPUTFILE
"
\
--rg-lib
"
$INPUTFILE
"
\
--rg-sample
"
$INPUTFILE
"
\
--index-prefix
/work/gad/shared/bin/lobstr/ref/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_
\
-o
"
$OUTPUTPREFIX
"
\
-v
lobstr_exitcode
=
$?
echo
"lobstr exit code :
$lobstr_exitcode
"
if
[
$lobstr_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
lobstr.failed
exit
1
fi
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
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