#!/bin/bash
set -e

pkg="clustalo"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi

cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP

/usr/bin/clustalo -i example.fa
/usr/bin/clustalo -i example.fa -o example.sto --outfmt=st
/usr/bin/clustalo -i example.fa	-o example.aln --outfmt=clu --force
/usr/bin/clustalo -i example.fa --guidetree-out=example.dnd --force
/usr/bin/clustalo -i example.fa	--guidetree-in=example.dnd
/usr/bin/clustalo -i example.sto
/usr/bin/clustalo -i example.sto  --dealign
/usr/bin/clustalo -i example.fa --iter=2
/usr/bin/clustalo -i example.fa --iter=5 --max-guidetree-iterations=1
/usr/bin/clustalo -i example.fa -o example.a2m -v

# Run example test from biopython
/usr/bin/clustalo -i f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force

echo "PASS"
