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#!/bin/bash
set -e
pkg=metabat
export LC_ALL=C.UTF-8
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/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
jgi_summarize_bam_contig_depths --referenceFasta contigs.fa --outputDepth contigs_depth.txt contigs-1000.fastq.bam
metabat1 --inFile contigs.fa --abdFile contigs_depth.txt --outFile contigs_bins -v
metabat2 --inFile contigs.fa --abdFile contigs_depth.txt --outFile contigs_bins -v
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