#!/bin/sh

# This is for running on EXPANSE

export MODULEPATH=/expanse/projects/ngbt/opt/expanse/modules:$MODULEPATH
module load mafft/7.505

MAFFTBINARY=mafft
/expanse/projects/ngbt/opt/expanse/slurm-aff $MAFFTBINARY &

case $1 in
                -qinsi)
                        shift; MAFFTBINARY=mafft-qinsi;;
                        #check that seed is a positive int
                -xinsi)
                        shift; MAFFTBINARY=mafft-xinsi;;
                        #check that num_chains is a positive int.
                *)
                        ;;
esac

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP" 1>&2
echo "CIPRES_NP=$CIPRES_NP" 1>&2

start=$(date +%s)
echo "running:" 1>&2
echo "${MAFFTBINARY} --progress ${PWD}/progress.mafft $*" 1>&2

${MAFFTBINARY} --progress ${PWD}/progress.mafft $*

echo 1>&2
end=$(date +%s)
elapsed=$((end-start))
echo elapsed = $elapsed s 1>&2

treeoutfile=*tree
if [ -f $treeoutfile ]
then chmod og+r *tree
fi