Add autopkgtest

unicycler (0.4.7+dfsg-2) UNRELEASED; urgency=medium

  * Team upload.

  [ Andreas Tille ]

  * Add manpages

  [ Liubov Chuprikova ]

  * Add autopkgtest

 -- Andreas Tille <tille@debian.org>  Wed, 24 Oct 2018 09:04:28 +0200

unicycler (0.4.7+dfsg-1) unstable; urgency=medium

Tests: run-unit-test

Depends: @

Depends: @, @builddeps@

Restrictions: allow-stderr

#!/bin/bash

set -e

pkg=#PACKAGENAME#

pkg=unicycler

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

if [ -d /usr/share/${pkg}-data/sample_data ] ; then

  cp -a /usr/share/${pkg}-data/sample_data/* $AUTOPKGTEST_TMP

else

  echo "Please install package unicycler-data to run this script"

  exit 1

fi

cd $AUTOPKGTEST_TMP

#do_stuff_to_test_package#

unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o illumina_assembly

#unicycler -l long_reads_high_depth.fastq.gz -o long_read_assembly

# This command fails with the following error:

#    Assembling contigs and long reads with miniasm

#    ...

#    Assembling reads with miniasm... empty result

#    Error: miniasm assembly failed

# It might be that the reads have not enough depth. See issue:

#    https://github.com/rrwick/Unicycler/issues/38

unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads_low_depth.fastq.gz -o hybrid_assembly

debian/tests/run-unit-test

debian/README.test