Mohd Bilal pushed to branch master at Debian Med / rockhopper
Commits: 0cfd21bf by Mohammed Bilal at 2022-07-14T12:25:35+00:00 Add example data as multi-orig tarball - - - - - fc0671d7 by Mohammed Bilal at 2022-07-14T12:26:31+00:00 New upstream version 2.0.3+dfsg2 - - - - - 16c10371 by Mohammed Bilal at 2022-07-14T12:26:50+00:00 Update upstream source from tag 'upstream/2.0.3+dfsg2' Update to upstream version '2.0.3+dfsg2' with Debian dir fd235a2cdf3440902782fc9ad46b12cd7a134108 - - - - - 5df01f6d by Mohammed Bilal at 2022-07-14T18:14:27+05:30 Add autopkgtests - - - - - 3dbc7582 by Mohammed Bilal at 2022-07-14T18:22:10+05:30 Add script to fetch test data - - - - - 95a3b141 by Mohammed Bilal at 2022-07-14T18:24:44+05:30 Add copyright for test data - - - - - 310fc555 by Mohammed Bilal at 2022-07-14T12:56:22+00:00 routine-update: Packaging update - - - - - 55c329f4 by Mohammed Bilal at 2022-07-14T12:56:27+00:00 routine-update: Standards-Version: 4.6.1 - - - - - 7042230f by Mohammed Bilal at 2022-07-14T12:57:11+00:00 routine-update: Ready to upload to unstable - - - - - a26f6963 by Mohammed Bilal at 2022-07-14T12:58:53+00:00 Update changelog - - - - - 11 changed files: - + debian-tests-data/Example_Condition1.fastq.gz - + debian-tests-data/Example_Condition2.fastq.gz - + debian-tests-data/Example_denovo.fastq.gz - debian/changelog - debian/control - debian/copyright - + debian/gbp.conf - + debian/tests/README - + debian/tests/control - + debian/tests/get-test-data - + debian/tests/run-unit-test Changes: ===================================== debian-tests-data/Example_Condition1.fastq.gz ===================================== Binary files /dev/null and b/debian-tests-data/Example_Condition1.fastq.gz differ ===================================== debian-tests-data/Example_Condition2.fastq.gz ===================================== Binary files /dev/null and b/debian-tests-data/Example_Condition2.fastq.gz differ ===================================== debian-tests-data/Example_denovo.fastq.gz ===================================== Binary files /dev/null and b/debian-tests-data/Example_denovo.fastq.gz differ ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +rockhopper (2.0.3+dfsg2-3) UNRELEASED; urgency=medium + + * Team upload. + * Add example data as multi-orig tarball + * New upstream version 2.0.3+dfsg2 + * Add autopkgtests + * Add script to fetch test data + * routine-update: Packaging update + * routine-update: Standards-Version: 4.6.1 + * routine-update: Ready to upload to unstable + + -- Mohammed Bilal <[email protected]> Thu, 14 Jul 2022 12:58:15 +0000 + rockhopper (2.0.3+dfsg2-2) unstable; urgency=medium * Source-only upload ===================================== debian/control ===================================== @@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13), javahelper, default-jdk, igv -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/rockhopper Vcs-Git: https://salsa.debian.org/med-team/rockhopper.git Homepage: https://cs.wellesley.edu/~btjaden/Rockhopper/ ===================================== debian/copyright ===================================== @@ -28,6 +28,10 @@ Files: * Copyright: 2013-2014 Brian Tjaden License: GPL-3+ +Files: debian-tests-data/* +Copyright: 2013-2014 Brian Tjaden +License: GPL-3+ + Files: debian/* Copyright: 2018 Andreas Tille <[email protected]> 2022 Pierre Gruet <[email protected]> ===================================== debian/gbp.conf ===================================== @@ -0,0 +1,4 @@ +[DEFAULT] +pristine-tar=True +filter=[ '.gitignore', '.travis.yml', '.git*' ] +component=['debian-tests-data'] ===================================== debian/tests/README ===================================== @@ -0,0 +1,6 @@ +Tests for rockhopper +================= + +The data for tests has been referenced from: + https://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html + ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/get-test-data ===================================== @@ -0,0 +1,8 @@ +#!/bin/bash +wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_Condition1.fastq +wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_Condition2.fastq +wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_denovo.fastq.gz +mkdir data && mv Example_* data/ +tarball=$(dpkg-parsechangelog --file ../changelog | awk '/^Source:/ {print $2}')_$(dpkg-parsechangelog --file ../changelog | awk '/^Version:/ {print $2}' | cut -f1 -d-).orig-debian-tests-data.tar.gz +tar --owner=root --group=root --mode=a+rX -cvzSf $tarball data +echo "Now move $tarball next to the new upstream tarball and gbp import it as usual" ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,31 @@ +#!/bin/bash +set -e + +pkg=rockhopper + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp debian-tests-data/* -a "${AUTOPKGTEST_TMP}/" + +cd "${AUTOPKGTEST_TMP}" + +echo "e65adc8788546540a70dac02e99bedd9 Rockhopper_Results/summary.txt" >> checksums +echo "4540bf9083d1149d7c158cfdd6d52e26 Rockhopper_Results/transcripts.txt" >> checksums +echo "9b130dbe2c1bab1baa97e80a3019c063 de_novo_results/summary.txt" >> checksums +echo "2c59b3787a789187975cf519b3833f43 de_novo_results/transcripts.txt" >> checksums + +echo -e "\e[93m\e[1mRunning Tests\e[0m" + +echo "Test 1" +rockhopper Example_Condition1.fastq.gz,Example_Condition2.fastq.gz + +echo "Test 2" +rockhopper Example_denovo.fastq.gz -o de_novo_results + +md5sum --check checksums + +echo -e "\e[92m\e[1mPASS\e[0m" View it on GitLab: https://salsa.debian.org/med-team/rockhopper/-/compare/0fc245b2f6793f9d57ecc4cf896b5da9041556c5...a26f6963675082ac8a7ba14df73dcead2351ad2c -- View it on GitLab: https://salsa.debian.org/med-team/rockhopper/-/compare/0fc245b2f6793f9d57ecc4cf896b5da9041556c5...a26f6963675082ac8a7ba14df73dcead2351ad2c You're receiving this email because of your account on salsa.debian.org.
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