2026-08-02

99.scripts/workflow/coalescence_network/bpp/run_bpp.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+# Script to run BPP A00 analysis for coalescence network inference
+
+# Set working directory
+WORK_DIR=$(pwd)
+SCRIPT_DIR="$(dirname "$0")"
+
+# Check if BPP is installed and available
+if ! command -v bpp &> /dev/null
+then
+    echo "Error: BPP is not installed or not in PATH"
+    echo "Please install BPP and make sure it's accessible in your PATH"
+    exit 1
+fi
+
+# Check if control file exists
+CONTROL_FILE="${SCRIPT_DIR}/run_bpp_a00.ctl"
+if [ ! -f "$CONTROL_FILE" ]; then
+    echo "Error: Control file not found at $CONTROL_FILE"
+    echo "Please make sure the control file exists"
+    exit 1
+fi
+
+echo "Starting BPP A00 analysis..."
+echo "Control file: $CONTROL_FILE"
+echo "Working directory: $WORK_DIR"
+
+# Run BPP analysis
+bpp --cfile "$CONTROL_FILE"
+
+# Check if the run was successful
+if [ $? -eq 0 ]; then
+    echo "BPP analysis completed successfully!"
+    
+    # Check for output files
+    JOBNAME=$(grep -E "^jobname\s*=" "$CONTROL_FILE" | sed -E 's/^jobname\s*=\s*(.*)/\1/' | tr -d ' ')
+    if [ -z "$JOBNAME" ]; then
+        JOBNAME="out"
+    fi
+    
+    echo "Output files:"
+    echo "  Main output: ${JOBNAME}.txt"
+    echo "  MCMC samples: ${JOBNAME}.mcmc.txt"
+    
+    if [ -f "${JOBNAME}.txt" ]; then
+        echo "Main output file created successfully"
+    else
+        echo "Warning: Main output file not found"
+    fi
+    
+    if [ -f "${JOBNAME}.mcmc.txt" ]; then
+        echo "MCMC samples file created successfully"
+    else
+        echo "Warning: MCMC samples file not found"
+    fi
+    
+else
+    echo "Error: BPP analysis failed"
+    exit 1
+fi