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Anne-Sophie Denommé-Pichon
STR
Commits
f930d128
Commit
f930d128
authored
Nov 03, 2019
by
Anne-Sophie Denommé-Pichon
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Change the output prefix and add time stamp in the name
parent
776de494
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3 changed files
with
4 additions
and
2 deletions
+4
-2
.gitignore
.gitignore
+2
-0
launch_expansionhunter.sh
launch_expansionhunter.sh
+1
-1
wrapper_expansionhunter.sh
wrapper_expansionhunter.sh
+1
-1
No files found.
.gitignore
View file @
f930d128
*~
*~
*.bam
*.bam
*.bai
*.bai
*.vcf
*.json
*.sh.o*
*.sh.o*
*.sh.po*
*.sh.po*
*.failed
*.failed
...
...
launch_expansionhunter.sh
View file @
f930d128
...
@@ -15,7 +15,7 @@
...
@@ -15,7 +15,7 @@
## Known bugs : None
## Known bugs : None
INPUTFILE
=
/archive/gad/shared/bam_new_genome_temp/dijen017.bam
INPUTFILE
=
/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX
=
test
OUTPUTPREFIX
=
/user1/gad/an1770de/Tools/ExpansionHunter/20191102/
"
$(
date
+
"%F_%H-%M-%S"
)
"
LOGFILE
=
/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
LOGFILE
=
/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
# Launch the script on local host with --local option and on SGE with qsub without the --local option
# Launch the script on local host with --local option and on SGE with qsub without the --local option
...
...
wrapper_expansionhunter.sh
View file @
f930d128
...
@@ -64,7 +64,7 @@ echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linu
...
@@ -64,7 +64,7 @@ echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linu
expansionhunter_exitcode
=
$?
expansionhunter_exitcode
=
$?
# Remove .bam and .bai symbolic links
# Remove .bam and .bai symbolic links
rm
"
$TMPDIR
/
$(
basenam
e
"
$INPUTFILE
"
)
"
rm
"
$TMPDIR
/
$(
basenam
e
"
$INPUTFILE
"
)
"
rm
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
rm
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
rmdir
"
$TMPDIR
"
rmdir
"
$TMPDIR
"
...
...
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