Pranav Ballaney pushed to branch master at Debian Med / bio-rainbow
Commits: f7f6d388 by Pranav Ballaney at 2020-08-23T05:14:06+05:30 Install data for autopkgtests - - - - - 8ca3ff30 by Pranav Ballaney at 2020-08-23T05:14:33+05:30 Add autopkgtests - - - - - dd7e3e90 by Pranav Ballaney at 2020-08-23T05:19:01+05:30 Install docs - - - - - 194fc3e8 by Pranav Ballaney at 2020-08-23T05:26:29+05:30 Add Pranav Ballaney to Uploaders - - - - - 9917fe5b by Pranav Ballaney at 2020-08-23T05:29:05+05:30 Update changelog - - - - - fa54a5d5 by Pranav Ballaney at 2020-08-23T05:29:58+05:30 routine-update: Standards-Version: 4.5.0 - - - - - 11cca782 by Pranav Ballaney at 2020-08-23T05:29:59+05:30 routine-update: debhelper-compat 13 - - - - - 539ec9d9 by Pranav Ballaney at 2020-08-23T05:30:00+05:30 routine-update: Remove trailing whitespace in debian/rules - - - - - 2a823259 by Pranav Ballaney at 2020-08-23T05:30:00+05:30 routine-update: Add salsa-ci file - - - - - 9f803384 by Pranav Ballaney at 2020-08-23T05:30:01+05:30 routine-update: Rules-Requires-Root: no - - - - - 61d31d44 by Pranav Ballaney at 2020-08-23T05:31:35+05:30 Include binaries - - - - - aeea114a by Pranav Ballaney at 2020-08-23T05:32:57+05:30 routine-update: Ready to upload to unstable - - - - - 13 changed files: - + debian/README.test - debian/changelog - − debian/compat - debian/control - debian/docs - + debian/examples - debian/rules - + debian/salsa-ci.yml - + debian/source/include-binaries - + debian/tests/control - + debian/tests/data/R.1.fastq.gz - + debian/tests/data/R.2.fastq.gz - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,18 @@ +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. + +Notes on the files used for testing this package. +───────────────────────────────────────────────── + +R.1.fasta and R.2.fasta were generated as random +sequences, using rangen from dazzdb and +artfastqgenerator by running the following commands: + + rangen 0.005 -r2020 > R.fasta + artfastqgenerator -O R -R R.fasta -S ">random" \ No newline at end of file ===================================== debian/changelog ===================================== @@ -1,3 +1,22 @@ +bio-rainbow (2.0.4+dfsg-2) unstable; urgency=medium + + [ Steffen Möller ] + * Updated bio.tools ref + * Added ref to conda + + [ Pranav Ballaney ] + * Install data for autopkgtests + * Add autopkgtests + * Install docs + * Add Pranav Ballaney to Uploaders + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Remove trailing whitespace in debian/rules (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Pranav Ballaney <[email protected]> Sun, 23 Aug 2020 05:32:47 +0530 + bio-rainbow (2.0.4+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -1,14 +1,16 @@ Source: bio-rainbow Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> +Uploaders: Olivier Sallou <[email protected]>, + Pranav Ballaney <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 13), help2man -Standards-Version: 4.1.4 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git Homepage: http://sourceforge.net/projects/bio-rainbow/ +Rules-Requires-Root: no Package: bio-rainbow Architecture: any ===================================== debian/docs ===================================== @@ -1,2 +1,3 @@ -README.txt -README.txt +README* +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/data/* \ No newline at end of file ===================================== debian/rules ===================================== @@ -10,7 +10,7 @@ include /usr/share/dpkg/default.mk export DEB_BUILD_MAINT_OPTIONS = hardening=+all %: - dh $@ + dh $@ override_dh_installman: # dh_installman is messing up .sh extension as language extension ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/source/include-binaries ===================================== @@ -0,0 +1,2 @@ +debian/tests/data/R.1.fastq.gz +debian/tests/data/R.2.fastq.gz \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data/R.1.fastq.gz ===================================== Binary files /dev/null and b/debian/tests/data/R.1.fastq.gz differ ===================================== debian/tests/data/R.2.fastq.gz ===================================== Binary files /dev/null and b/debian/tests/data/R.2.fastq.gz differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,29 @@ +#!/bin/bash +set -e + +pkg=bio-rainbow + +export LC_ALL=C.UTF-8 +if [ "${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}" + +gunzip -r * + +bio-rainbow cluster -1 R.1.fastq -2 R.2.fastq > rbcluster.out 2> log +bio-rainbow div -i rbcluster.out -o rbdiv.out +bio-rainbow merge -o rbasm.out -a -i rbdiv.out -N50000 + +echo "4f0a35450f64adc3bfd6f4b664887631 rbasm.out" >> checksums +echo "29a755de547ac393328c8b31d5f6e26d rbcluster.out" >> checksums +echo "b7dfd0cfd2f0eade15487a72632e972d rbdiv.out" >> checksums + +md5sum --check checksums \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea -- View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea You're receiving this email because of your account on salsa.debian.org.
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