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#!/bin/bash
set -e
pkg=skewer
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}"
skewer -x TCGTATGCCGTCTTCTGCTTGT -l 16 -L 30 -d 0 -o output data.fastq.gz
skewer -Q 9 -t 2 -x adapters.fa data.fastq.gz -o trimmed
if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
then
echo "52d871b7c71f7e931ba8b1cee489e210 trimmed-trimmed.fastq" >> checksums
md5sum --check checksums
echo "Expected output and generated output are same!"
else
[ -s "trimmed-trimmed.fastq" ] || exit 1
fi
# Check that logging happens
for f in *.log
do
echo "$f"
[ -s $f ] || exit 1
done
echo "PASS"
|
