Pranav Ballaney pushed to branch master at Debian Med / nanook
Commits: 54ed425d by Pranav Ballaney at 2020-06-28T04:53:02+05:30 Add test and reference data - - - - - 59b3abc6 by Pranav Ballaney at 2020-06-28T04:53:25+05:30 Add autopkgtests - - - - - a76719c5 by Pranav Ballaney at 2020-06-28T04:53:57+05:30 Install docs - - - - - 9 changed files: - + debian/README.test - debian/changelog - + debian/docs - + debian/examples - + debian/tests/README.test_data - + debian/tests/control - + debian/tests/data.tar.gz - + debian/tests/ref.tar.gz - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,18 @@ +nanook (1.33+dfsg-2) UNRELEASED; urgency=medium + + [ Hervé Ménager ] + * correct bio.tools and scicrunch refs + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Pranav Ballaney ] + * Add test and reference data + * Add autopkgtests + * Install docs + + -- Pranav Ballaney <[email protected]> Sun, 28 Jun 2020 04:53:32 +0530 + nanook (1.33+dfsg-1) unstable; urgency=medium * New upstream version ===================================== debian/docs ===================================== @@ -0,0 +1,4 @@ +README.md +debian/README* +debian/tests/run-unit-test +debian/tests/README* ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/* \ No newline at end of file ===================================== debian/tests/README.test_data ===================================== @@ -0,0 +1,5 @@ +data.tar.gz is a subset of the data available at +https://opendata.earlham.ac.uk/opendata/nanook/nanook_ecoli_500.tar.gz + +ref.tar.gz contains results obtained by processing this data as described at +https://nanook.readthedocs.io/en/latest/tutorial.html \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data.tar.gz ===================================== Binary files /dev/null and b/debian/tests/data.tar.gz differ ===================================== debian/tests/ref.tar.gz ===================================== Binary files /dev/null and b/debian/tests/ref.tar.gz differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,35 @@ +#!/bin/bash +set -e + +pkg=nanook + +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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +tar xf data.tar.gz +tar xf ref.tar.gz +#do_stuff_to_test_package# +cd data/nanook_ecoli_500/references +lastdb -Q 0 ecoli_dh10b_cs ecoli_dh10b_cs.fasta +cd .. +nanook extract -s N79596_dh10b_8kb_11022015 +nanook align -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta +nanook analyse -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta -passonly + +cd ../.. +for file in ref/*; do + if [[ -f $file ]]; then + output=data${file#ref} + diff $file $output + fi +done View it on GitLab: https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490 -- View it on GitLab: https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490 You're receiving this email because of your account on salsa.debian.org.
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