Nilesh Patra pushed to branch master at Debian Med / allelecount
Commits: 385b4b73 by Nilesh Patra at 2020-10-03T20:36:21+05:30 New upstream version 4.2.0 - - - - - abc39e75 by Nilesh Patra at 2020-10-03T20:36:21+05:30 routine-update: New upstream version - - - - - aec5af90 by Nilesh Patra at 2020-10-03T20:36:26+05:30 Update upstream source from tag 'upstream/4.2.0' Update to upstream version '4.2.0' with Debian dir f768b94517fe5f4dbd1a5d5dabaf3c1858915a6f - - - - - 1c5e7e18 by Nilesh Patra at 2020-10-03T20:36:26+05:30 routine-update: debhelper-compat 13 - - - - - 41da495c by Nilesh Patra at 2020-10-03T20:36:32+05:30 routine-update: Ready to upload to unstable - - - - - 1192ebec by Nilesh Patra at 2020-10-03T20:59:48+05:30 Add autopkgtests - - - - - 7 changed files: - CHANGES.md - debian/changelog - debian/control - + debian/tests/control - + debian/tests/run-unit-test - perl/lib/Sanger/CGP/AlleleCount.pm - setup.sh Changes: ===================================== CHANGES.md ===================================== @@ -1,5 +1,9 @@ # CHANGES +## v4.2.0 + +* Updated to hstlib 1.11 + ## v4.1.0 * Created Docker file and build scripts to generate a containeraized code ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +allelecount (4.2.0-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * debhelper-compat 13 (routine-update) + * Add autopkgtests + + -- Nilesh Patra <[email protected]> Sat, 03 Oct 2020 20:36:32 +0530 + allelecount (4.1.0-3) unstable; urgency=medium * Just use Build-Depends to enable build time testing ===================================== debian/control ===================================== @@ -4,7 +4,7 @@ Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional Testsuite: autopkgtest-pkg-perl -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), libhts-dev, libbz2-dev, libconst-fast-perl <!nocheck>, ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,26 @@ +#!/bin/bash +set -e + +CUR_DIR=`pwd` +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cd "${AUTOPKGTEST_TMP}" +cp -a ${CUR_DIR}/testData/* . + +echo "Testing C binary" +alleleCounter -l test10X.loci -b test10X.bam -o test1 -m 2 -r test10X.bam.bai +echo "PASS" + +echo "Test Perl counterpart" +alleleCounter.pl -l test10X.loci -b test10X.bam -o test2 -m 2 -r test10X.bam.bai +echo "PASS" + +echo "Check if both are same" +diff -u test1 test2 +rm -f ./test1 ./test2 +echo "PASS" + ===================================== perl/lib/Sanger/CGP/AlleleCount.pm ===================================== @@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount; use strict; use base 'Exporter'; -our $VERSION = '4.1.0'; +our $VERSION = '4.2.0'; our @EXPORT = qw($VERSION); 1; ===================================== setup.sh ===================================== @@ -21,7 +21,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. ##########LICENCE########## -SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"; +SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2"; EXP_SAMV="1.3.1" View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80 -- View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
