Liubov Chuprikova pushed to branch master at Debian Med / unicycler
Commits: b0b0cac3 by Liubov Chuprikova at 2018-10-27T17:07:15Z Add autopkgtest - - - - - 4 changed files: - debian/changelog - debian/tests/control - debian/tests/run-unit-test - + debian/unicycler.docs Changes: ===================================== debian/changelog ===================================== @@ -1,7 +1,13 @@ unicycler (0.4.7+dfsg-2) UNRELEASED; urgency=medium + * Team upload. + + [ Andreas Tille ] * Add manpages + [ Liubov Chuprikova ] + * Add autopkgtest + -- Andreas Tille <[email protected]> Wed, 24 Oct 2018 09:04:28 +0200 unicycler (0.4.7+dfsg-1) unstable; urgency=medium ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @ +Depends: @, @builddeps@ Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -1,15 +1,32 @@ #!/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/unicycler.docs ===================================== @@ -0,0 +1,2 @@ +debian/tests/run-unit-test +debian/README.test View it on GitLab: https://salsa.debian.org/med-team/unicycler/commit/b0b0cac3438024c8c2ae609d255e10f08fa45e1c -- View it on GitLab: https://salsa.debian.org/med-team/unicycler/commit/b0b0cac3438024c8c2ae609d255e10f08fa45e1c You're receiving this email because of your account on salsa.debian.org.
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