#! /bin/bash
# sh -> bash for debian. By J. R. Peterson. 2015/Jun.

#modified by BF for BIRCH
#pushd "`dirname "$0"`" > /dev/null 2>&1; rootdir="$PWD"; export rootdir; popd > /dev/null 2>&1;
#MAFFT_BINARIES="$rootdir"/mafftdir/libexec; export MAFFT_BINARIES;
MAFFT_BINARIES="$BIRCH/bin-$BIRCH_PLATFORM/mafftdir/libexec"; export MAFFT_BINARIES;

arguments=""
while [ $# -gt 1 ];
do
	arguments=$arguments" "$1
	shift
done

"$BIRCH/bin-$BIRCH_PLATFORM/mafftdir/bin/einsi" $arguments "$1"
# $1 can have space in file name