60 lines
1.5 KiB
Bash
Executable File
60 lines
1.5 KiB
Bash
Executable File
#!/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 |