#!/bin/bash

# This wrapper is for running 1 chain of StatAlign 3.4 on Expanse.

# Load bali-phy to access trees-consensus postprocessor
export MODULEPATH=/expanse/projects/ngbt/opt/expanse/modules:$MODULEPATH
module load bali-phy/3.6.1

start=$(date +%s)
echo "running statalign $*"
echo
java -Xmx8g -jar /expanse/projects/ngbt/opt/expanse/statalign/3.4/StatAlign.jar $*

# Convert trees from NEXUS to newick format
grep tree infile.tree | awk '{print $4}' > infile.tree.newick

trees-consensus infile.tree.newick > infile.tree.consensus
echo
end=$(date +%s)
elapsed=$((end-start))
echo elapsed = $elapsed s