#! /bin/bash
set -e
if [ "$#" -ne 4 ]; then
    echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
    echo "Run modeltest-ng and raxml-ng on a given alignment"
    exit 1
fi

aln=$(readlink -f "$1")
out=$2
threads=$3
outgroup=$4
outdir=$(dirname "$out")
mkdir -p "$outdir"
# run modeltest-ng
modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
# run raxml-ng
cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
bash -c "$cmd $params" >/dev/null