#!/bin/bash
set -e

pkg="physamp"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/share/doc/${pkg}/examples/PF01049/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;

bppalnoptim param=AlnOptimFasttree.bpp
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=complete
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=single
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=average
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=median
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=centroid
bppalnoptim param=AlnOptimAuto.bpp LINKAGE=ward

#Get a selection of sequences:
bppalnoptim param=AlnOptimFasttreeStop.bpp

echo "PASS"
