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Anne-Sophie Denommé-Pichon
STR
Commits
3126d143
Commit
3126d143
authored
Jun 11, 2021
by
Anne-Sophie Denommé-Pichon
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Handle path to Python 3
parent
806b712b
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4 changed files
with
6 additions
and
4 deletions
+6
-4
config.sh
config.sh
+2
-0
launch_results.sh
launch_results.sh
+1
-1
launch_str_outliers.sh
launch_str_outliers.sh
+1
-1
wrapper_ehdn_outlier.sh
wrapper_ehdn_outlier.sh
+2
-2
No files found.
config.sh
View file @
3126d143
...
...
@@ -19,6 +19,8 @@ COMPUTE_QUEUE=batch
TRANSFER
=
yes
# Tools
PYTHON
=
"/work/gad/shared/bin/python3.6/python3"
PARALLEL
=
"/work/gad/shared/bin/parallel/parallel-20150522-1.el7.cern/bin/parallel"
PARALLEL_JOB_COUNT
=
"16"
...
...
launch_results.sh
View file @
3126d143
...
...
@@ -24,7 +24,7 @@ fi
mkdir
-p
"
$RESULTS_OUTPUTDIR
"
# Launch getResults.py
"
$(
dirname
"
$0
"
)
/getResults.py"
"
$SAMPLES
"
"
$
PYTHON
"
"
$
(
dirname
"
$0
"
)
/getResults.py"
"
$SAMPLES
"
# Launch launch_str_outliers.sh
"
$(
dirname
"
$0
"
)
/launch_str_outliers.sh"
"
$SAMPLES
"
...
...
launch_str_outliers.sh
View file @
3126d143
...
...
@@ -28,6 +28,6 @@ cd "$RESULTS_OUTPUTDIR" || exit 1
for
locus_tsv
in
$(
ls
*
.tsv |
grep
-v
outliers
)
;
do
locus
=
"
$(
basename
"
$locus_tsv
"
".tsv"
)
"
echo
"Processing
$locus
"
>
&2
"
$SCRIPT
"
"
$locus
"
"
$SAMPLES
"
>
"
$locus
.outliers.tsv"
"
$
PYTHON
"
"
$
SCRIPT
"
"
$locus
"
"
$SAMPLES
"
>
"
$locus
.outliers.tsv"
done
wrapper_ehdn_outlier.sh
View file @
3126d143
...
...
@@ -75,7 +75,7 @@ then
fi
# Run locus-based comparison analysis
"
$EHDN_OUTLIER
"
locus
\
"
$
PYTHON
"
"
$
EHDN_OUTLIER
"
locus
\
--manifest
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.outlier_locus.tsv"
...
...
@@ -91,7 +91,7 @@ fi
# Run motif_based comparison analysis
"
$EHDN_OUTLIER
"
motif
\
"
$
PYTHON
"
"
$
EHDN_OUTLIER
"
motif
\
--manifest
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$OUTPUTDIR
/
$CASE
/str/ehdn/
$CASE
.outlier_motif.tsv"
...
...
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