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#!/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"
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