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Anne-Sophie Denommé-Pichon
STR
Commits
776de494
Commit
776de494
authored
Nov 03, 2019
by
Anne-Sophie Denommé-Pichon
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Add --local option to the wrapper launcher for ExpansionHunter
parent
f6feb237
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launch_expansionhunter.sh
launch_expansionhunter.sh
+7
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launch_expansionhunter.sh
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776de494
...
...
@@ -18,8 +18,10 @@ 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
# 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
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_expansionhunter.sh"
else
qsub
-pe
smp 1
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_expansionhunter.sh
fi
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