#! /bin/bash
set -e
SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
THREADS=${THREADS:-3}

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <in_dir> <out_dir> <ext>"
    echo "Run raxml-ng on filtered orthogroup alignments"
    exit 1
fi

in_dir=$(readlink -f "$1")
out_dir=$2
ext=$3
mkdir -p "$out_dir"
echo -n >raxml.cmds
for i in "$in_dir"/*."$ext"; do
    j=$(basename "$i" ."$ext")
    out_prefix="$out_dir/${j}/${j}"
    echo "$SCRIPTS/miscs/raxml.sh $i $out_prefix 4 Zju" >>raxml.cmds
done
xargs -t -P "$THREADS" -I cmd -a raxml.cmds bash -c "cmd"
echo "Raxml-ng all completed."