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Anne-Sophie Denommé-Pichon
STR
Commits
b38301db
Commit
b38301db
authored
Nov 03, 2019
by
Anne-Sophie Denommé-Pichon
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Change local output directory and add time stamp in log file names
parent
7264b1f2
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2 changed files
with
8 additions
and
4 deletions
+8
-4
launch_expansionhunter.sh
launch_expansionhunter.sh
+5
-2
launch_tredparse.sh
launch_tredparse.sh
+3
-2
No files found.
launch_expansionhunter.sh
View file @
b38301db
...
...
@@ -15,12 +15,15 @@
## Known bugs : None
INPUTFILE
=
/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX
=
/user1/gad/an1770de/Tools/ExpansionHunter/20191102/
"
$(
date
+
"%F_%H-%M-%S"
)
"
LOGFILE
=
/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/user1/gad/an1770de/Analyses/ExpansionHunter/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$DATE
"
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
"
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
...
...
launch_tredparse.sh
View file @
b38301db
...
...
@@ -14,9 +14,10 @@
## last revision date : 20191103
## Known bugs : None
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
INPUTFILE
=
/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTDIR
=
/user1/gad/an1770de/Tools/Tredparse/
"
$(
date
+
"%F_%H-%M-%S"
)
"
LOGFILE
=
"
$OUTPUTDIR
/
log
.log"
OUTPUTDIR
=
"/user1/gad/an1770de/Analyses/Tredparse/
$DATE
"
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
]
...
...
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