#!/bin/bash

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

# 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

# Change the value of seed for the second chain.
option0=$*
if [[ $option0 =~ "-seed=" ]]; then
  option1=""
  array=($option0)
  length=${#array[@]}
  for (( i=0; i<${length}; i++ ));
  do
    field=${array[i]}
    if [[ $field =~ "-seed=" ]]; then
      value=$(echo $field | sed -e 's/-seed=//g')
      value=$(( $value + 1 ))
      field="-seed=$value"
    fi
    option1="$option1 $field"
  done
else  
  field0="-seed=1"
  field1="-seed=2"
  option0="$field0 $*"
  option1="$field1 $*"
fi

# Add suffices to infile in option lists.
option0=$(echo $option0 | sed -e 's/infile/infile.chain0/g')
option1=$(echo $option1 | sed -e 's/infile/infile.chain1/g')

# Make two copies of infile.
cp -p infile infile.chain0
cp -p infile infile.chain1

start=$(date +%s)
echo "running statalign $option0" > chain0.out
echo >> chain0.out
java -Xmx8g -jar /expanse/projects/ngbt/opt/expanse/statalign/3.4/StatAlign.jar $option0 >> chain0.out &
echo "running statalign $option1" > chain1.out
echo >> chain1.out
java -Xmx8g -jar /expanse/projects/ngbt/opt/expanse/statalign/3.4/StatAlign.jar $option1 >> chain1.out
sleep 60

rm infile.chain0
rm infile.chain1

# 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