#!/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
