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Anne-Sophie Denommé-Pichon
STR
Commits
49c1f48d
Commit
49c1f48d
authored
Nov 18, 2019
by
Anne-Sophie Denommé-Pichon
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6 changed files
with
13 additions
and
12 deletions
+13
-12
launch_expansionhunter.sh
launch_expansionhunter.sh
+2
-2
launch_gangstr.sh
launch_gangstr.sh
+3
-3
launch_hipstr.sh
launch_hipstr.sh
+2
-2
launch_lobstr.sh
launch_lobstr.sh
+2
-2
launch_tredparse.sh
launch_tredparse.sh
+2
-2
wrapper_hipstr.sh
wrapper_hipstr.sh
+2
-1
No files found.
launch_expansionhunter.sh
View file @
49c1f48d
...
@@ -14,7 +14,7 @@
...
@@ -14,7 +14,7 @@
## last revision date : 20191102
## last revision date : 20191102
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/
archive/gad/shared/bam_new_genome_temp
/dijen017.bam
INPUTFILE
=
/
work/gad/shared/analyse/STR/Data/dijen017/dijen017
/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/ExpansionHunter/
$DATE
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/ExpansionHunter/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
...
@@ -27,5 +27,5 @@ then
...
@@ -27,5 +27,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_expansionhunter.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_expansionhunter.sh"
else
else
mkdir
-p
"
$OUTPUTDIR
"
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-
q
transfer
-
v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_expansionhunter.sh
qsub
-pe
smp 1
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_expansionhunter.sh
fi
fi
launch_gangstr.sh
View file @
49c1f48d
...
@@ -11,10 +11,10 @@
...
@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## Creation Date : 20191104
## last revision date : 201911
04
## last revision date : 201911
17
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/
archive/gad/shared/bam_new_genome_temp
/dijen017.bam
INPUTFILE
=
/
work/gad/shared/analyse/STR/Data/dijen017/dijen017
/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/GangSTR/
$DATE
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/GangSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
...
@@ -27,5 +27,5 @@ then
...
@@ -27,5 +27,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_gangstr.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_gangstr.sh"
else
else
mkdir
-p
"
$OUTPUTDIR
"
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_gangstr.sh
qsub
-pe
smp 1
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_gangstr.sh
fi
fi
launch_hipstr.sh
View file @
49c1f48d
...
@@ -14,7 +14,7 @@
...
@@ -14,7 +14,7 @@
## last revision date : 20191104
## last revision date : 20191104
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/
archive/gad/shared/bam_new_genome_temp
/dijen017.bam
INPUTFILE
=
/
work/gad/shared/analyse/STR/Data/dijen017/dijen017
/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/HipSTR/
$DATE
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/HipSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
-s
.bam
"
$INPUTFILE
"
)
_
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
-s
.bam
"
$INPUTFILE
"
)
_
$DATE
"
...
@@ -28,5 +28,5 @@ then
...
@@ -28,5 +28,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTFILE
=
"
$OUTPUTFILE
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_hipstr.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTFILE
=
"
$OUTPUTFILE
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_hipstr.sh"
else
else
mkdir
-p
"
$OUTPUTDIR
"
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp
1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_hipstr.sh
qsub
-pe
smp
2
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTFILE
=
"
$OUTPUTFILE
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_hipstr.sh
fi
fi
launch_lobstr.sh
View file @
49c1f48d
...
@@ -14,7 +14,7 @@
...
@@ -14,7 +14,7 @@
## last revision date : 20191104
## last revision date : 20191104
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/
archive/gad/shared/bam_new_genome_temp
/dijen017.bam
INPUTFILE
=
/
work/gad/shared/analyse/STR/Data/dijen017/dijen017
/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/LobSTR/
$DATE
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/LobSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
...
@@ -27,5 +27,5 @@ then
...
@@ -27,5 +27,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_lobstr.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_lobstr.sh"
else
else
mkdir
-p
"
$OUTPUTDIR
"
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp
1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_lobstr.sh
qsub
-pe
smp
4
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_lobstr.sh
fi
fi
launch_tredparse.sh
View file @
49c1f48d
...
@@ -14,7 +14,7 @@
...
@@ -14,7 +14,7 @@
## last revision date : 20191103
## last revision date : 20191103
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/
archive/gad/shared/bam_new_genome_temp
/dijen017.bam
INPUTFILE
=
/
work/gad/shared/analyse/STR/Data/dijen017/dijen017
/dijen017.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/Tredparse/
$DATE
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/Tredparse/
$DATE
"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
.log"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
.log"
...
@@ -26,5 +26,5 @@ then
...
@@ -26,5 +26,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTDIR
=
"
$OUTPUTDIR
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_tredparse.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTDIR
=
"
$OUTPUTDIR
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_tredparse.sh"
else
else
mkdir
-p
"
$OUTPUTDIR
"
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp
1
-q
transfer
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_tredparse.sh
qsub
-pe
smp
4
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_tredparse.sh
fi
fi
wrapper_hipstr.sh
View file @
49c1f48d
...
@@ -50,9 +50,10 @@ echo "command : FIXME"
...
@@ -50,9 +50,10 @@ echo "command : FIXME"
/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR
\
/work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR
\
--bams
"
$INPUTFILE
"
\
--bams
"
$INPUTFILE
"
\
--fasta
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--fasta
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions
/work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
\
--str-vcf
"
$OUTPUTFILE
"
--str-vcf
"
$OUTPUTFILE
"
# --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
hipstr_exitcode
=
$?
hipstr_exitcode
=
$?
echo
"hipstr exit code :
$hipstr_exitcode
"
echo
"hipstr exit code :
$hipstr_exitcode
"
...
...
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