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#!/bin/sh -e
pkg=kraken
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test_data/* .
gunzip -r *
kraken-build --add-to-library Acartia_tonsa.fasta --db test_db
kraken-build --add-to-library Acinetobacter_phage.fasta --db test_db
kraken-build --build --minimizer-len 5 --db test_db
kraken --db test_db test.fa > kraken.output
kraken-report --db test_db kraken.output
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