Handle path to Python 3

config.sh

@@ -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

@@ -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

@@ -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

@@ -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"