Andreas Tille pushed to branch master at Debian Med / fieldbioinformatics
Commits: 0a85c1b2 by Andreas Tille at 2020-06-22T14:19:15+02:00 Step forward with some autopkgtest. Please note: The current test script is requiring downloading data which is not possible at build time. But as far as I learned it can be done in autopkgtest. But it should be tested on a local machine first - - - - - 4 changed files: - debian/control - + debian/fieldbioinformatics-examples.install - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/control ===================================== @@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Malihe Asemani <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (=12), python3-all, python3-setuptools, dh-python +Build-Depends: debhelper-compat (=12), python3, python3-setuptools, dh-python Standards-Version: 4.1.3 Vcs-Browser: https://salsa.debian.org/med-team/fieldbioinformatics Vcs-Git: https://salsa.debian.org/med-team/fieldbioinformatics.git Homepage: https://github.com/artic-network/fieldbioinformatics Package: fieldbioinformatics -Architecture: any +Architecture: all Depends: ${python3:Depends}, ${misc:Depends} Description: pipeline for working with virus sequencing data sequenced with nanopore @@ -19,3 +19,17 @@ Description: pipeline for working with virus sequencing data sequenced with nano protocol to take the output from the sequencing protocol to consensus genome sequences. Includes basecalling, de-multiplexing, mapping, polishing and consensus generation. + +Package: fieldbioinformatics-examples +Architecture: all +Depends: ${python3:Depends}, + ${misc:Depends} +Enhances: fieldbioinformatics +Description: pipeline for working with virus sequencing data sequenced with nanopore (examples) + This is the ARTIC bioinformatics pipeline for working with virus sequencing + data, sequenced with nanopore. Nanopore is a complete bioinformatics + protocol to take the output from the sequencing protocol to consensus + genome sequences. Includes basecalling, de-multiplexing, mapping, polishing + and consensus generation. + . + This package contains some example data. ===================================== debian/fieldbioinformatics-examples.install ===================================== @@ -0,0 +1 @@ +test* usr/share/doc/fieldbioinformatics/examples ===================================== debian/rules ===================================== @@ -21,8 +21,8 @@ export PYBUILD_NAME=fieldbioinformatics %: dh $@ --with python3 --buildsystem=pybuild -### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected -#override_dh_auto_test: -#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) -# do_stuff_for_testing -#endif +override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + echo "Test is downloading extra data and thus can not be running here" + # ./test-runner.sh nanopolish +endif ===================================== debian/tests/run-unit-test ===================================== @@ -1,14 +1,11 @@ #!/bin/bash set -e -pkg=#PACKAGENAME# +pkg=fieldbioinformatics export LC_ALL=C.UTF-8 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) - # Double quote below to expand the temporary directory variable now versus - # later is on purpose. - # shellcheck disable=SC2064 trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM fi @@ -16,4 +13,6 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" cd "${AUTOPKGTEST_TMP}" -#do_stuff_to_test_package# +gunzip -r * + +bash ./test-runner.sh nanopolish View it on GitLab: https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9 -- View it on GitLab: https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9 You're receiving this email because of your account on salsa.debian.org.
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