Mohd Bilal pushed to branch master at Debian Med / tvc
Commits: ca557181 by Mohammed Bilal at 2022-09-05T22:43:41+05:30 Add autopkgtests - - - - - 869efd9c by Mohammed Bilal at 2022-09-05T17:17:52+00:00 routine-update: Packaging update - - - - - 129181bc by Mohammed Bilal at 2022-09-05T17:17:57+00:00 routine-update: Standards-Version: 4.6.1 - - - - - 1f1b495c by Mohammed Bilal at 2022-09-05T17:17:58+00:00 routine-update: debhelper-compat 13 - - - - - 421bdcb7 by Mohammed Bilal at 2022-09-05T17:18:05+00:00 routine-update: Add salsa-ci file - - - - - 14e4c45c by Mohammed Bilal at 2022-09-05T17:19:06+00:00 Set upstream metadata fields: Bug-Database, Bug-Submit. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html - - - - - 9abc9037 by Mohammed Bilal at 2022-09-05T17:21:28+00:00 Update changelog - - - - - 6 changed files: - debian/changelog - debian/control - + debian/salsa-ci.yml - + debian/tests/control - + debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +tvc (5.0.3+git20151221.80e144e+dfsg-5) UNRELEASED; urgency=medium + + * Team upload. + * Add autopkgtest + * Standards-Version: 4.6.1 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit. + + -- Mohammed Bilal <[email protected]> Mon, 05 Sep 2022 17:20:03 +0000 + tvc (5.0.3+git20151221.80e144e+dfsg-4) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -4,14 +4,14 @@ Uploaders: Dominique Belhachemi <[email protected]>, Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev -Standards-Version: 4.5.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Homepage: http://ioncommunity.thermofisher.com ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,32 @@ +#!/bin/bash +set -e + +pkg=TVC + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/${pkg}/examples/example1/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +echo -e "Running Tests" + +variant_caller_pipeline.py \ + --input-bam test.bam \ + --reference-fasta reference.fasta \ + --region-bed test_merged_plain.bed \ + --primer-trim-bed test_unmerged_detail.bed + +if [ -f TSVC_variants.vcf ] && \ + [ -f small_variants.vcf ] && \ + [ -f small_variants_filtered.vcf ]; then + + echo "PASS" + +else + echo "FAIL" +fi ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Bug-Database: https://github.com/domibel/IonTorrent-VariantCaller/issues +Bug-Submit: https://github.com/domibel/IonTorrent-VariantCaller/issues/new Registry: - Name: OMICtools Entry: OMICS_29293 View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/ab703348ee8a5d3f1cb4f6f75b1221d87150c920...9abc9037641bafb32bf980da6563397b7a62e904 -- View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/ab703348ee8a5d3f1cb4f6f75b1221d87150c920...9abc9037641bafb32bf980da6563397b7a62e904 You're receiving this email because of your account on salsa.debian.org.
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