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

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <input_fasta_dir> <extension> <output_dir>"
    echo "Run MrBayes for each fasta file in the input directory"
    exit 1
fi

input_dir=$(readlink -f "$1")
ext=$2
output_dir=$(readlink -f "$3")
mkdir -p "${output_dir}"
echo -n >mrbayes.cmds
for f in "${input_dir}"/*."${ext}"; do
    j=$(basename "$f" ."${ext}")
    echo "bash $SCRIPTS/miscs/mrbayes.sh $f ${output_dir}/${j}/${j}.nex" >>mrbayes.cmds
done
xargs -t -P 12 -I cmd -a mrbayes.cmds bash -c "cmd"
echo "All MrBayes analyses are done!"