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Anne-Sophie Denommé-Pichon
STR
Commits
7a5daf35
Commit
7a5daf35
authored
Nov 04, 2019
by
Anne-Sophie Denommé-Pichon
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Create script to launch GangSTR wrapper
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2db647fe
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launch_gangstr.sh
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7a5daf35
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing GangSTR 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/GangSTR/
$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_gangstr.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_gangstr.sh
fi
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