#! /bin/bash
set -e
SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
THREADS=${THREADS:-16}

if [ "$#" -ne 4 ]; then
    echo "Usage: $0 <aln_dir> <ml_dir> <out_dir> <alignment_ext>"
    echo "Run MCMCtree on orthogroup alignments with corresponding ML trees"
    exit 1
fi

aln_dir=$1
ml_dir=$2
out_dir=$3
ext=$4
mkdir -p "$out_dir"
echo -n >mcmctree.cmds
ctlfile=$(readlink -f "$SCRIPTS/miscs/mcmctree.ctl")
for i in "$aln_dir"/*."$ext"; do
    j=$(basename "$i" ."$ext")
    aln=$(readlink -f "$i")
    ml_tree=$(readlink -f "$ml_dir/${j}/${j}.raxml.bestTree")
    mkdir -p "${out_dir}/${j}"
    cmd="cd ${out_dir}/${j} && Rscript $SCRIPTS/miscs/mcmctree_workflow.r"
    params="-a $aln -t $ml_tree -c ${ctlfile} -p ${j}"
    echo "$cmd $params > mcmctree.log 2>&1" >>mcmctree.cmds
done
xargs -t -P "$THREADS" -I cmd -a mcmctree.cmds bash -c "cmd"
echo "MCMCtree all completed."