#!/bin/bash

# This wrapper is for running 2 chains of StatAlign 3.4 in parallel using MPI on Expanse.

STATALIGN_JAR=/expanse/projects/ngbt/opt/expanse/statalign/3.4/StatAlign.jar
export MPJ_HOME=/expanse/projects/ngbt/opt/expanse/statalign/3.4/lib/mpj-v0_44

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

start=$(date +%s)
echo "running statalign $*"
echo
java -Xmx16g -jar $MPJ_HOME/lib/starter.jar -np 2 -cp $STATALIGN_JAR statalign.StatAlignParallel $*
sleep 10

# Convert trees from NEXUS to newick format
grep tree infile.chain0.tree | awk '{print $4}' > infile.chain0.tree.newick
grep tree infile.chain1.tree | awk '{print $4}' > infile.chain1.tree.newick

trees-consensus infile.chain0.tree.newick > infile.chain0.tree.consensus
trees-consensus infile.chain1.tree.newick > infile.chain1.tree.consensus
echo
trees-bootstrap infile.chain0.tree.newick infile.chain1.tree.newick | grep ASDSF
echo
end=$(date +%s)
elapsed=$((end-start))
echo elapsed = $elapsed s