Handle path to Python 3

parent 806b712b
......@@ -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"
......
......@@ -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"
......
......@@ -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
......@@ -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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