#!/bin/sh

# Can't run module command (I think it's a bash fn) without sourcing bashrc
source $HOME/.bashrc

module load mafft

MAFFTBINARY=mafft

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
echo "running:" 1>&2
echo "${MAFFTBINARY} --progress ${PWD}/progress.mafft $*" 1>&2

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