Andreas Tille pushed to branch master at Debian Med / biobambam2
Commits: 375596d4 by Andreas Tille at 2019-04-12T09:18:23Z Initial packaging - - - - - 12 changed files: - + debian/README.test - + debian/changelog - + debian/compat - + debian/control - + debian/copyright - + debian/lintian-overrides - + debian/rules - + debian/source/format - + debian/tests/control - + debian/tests/run-unit-test - + debian/upstream/metadata - + debian/watch 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 ===================================== @@ -0,0 +1,6 @@ +biobambam2 (2.0.95-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #<bug>) + TODO: https://salsa.debian.org/med-team/libmaus2 + + -- Andreas Tille <[email protected]> Fri, 12 Apr 2019 10:26:19 +0200 ===================================== debian/compat ===================================== @@ -0,0 +1 @@ +12 ===================================== debian/control ===================================== @@ -0,0 +1,32 @@ +Source: biobambam2 +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 12~), + pkg-config +Standards-Version: 4.3.0 +Vcs-Browser: https://salsa.debian.org/med-team/biobambam2 +Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git +Homepage: https://gitlab.com/german.tischler/biobambam2 + +Package: biobambam2 +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: tools for early stage alignment file processing + This package contains some tools for processing BAM files including + . + bamsormadup: parallel sorting and duplicate marking + bamcollate2: reads BAM and writes BAM reordered such that alignment + or collated by query name + bammarkduplicates: reads BAM and writes BAM with duplicate alignments + marked using the BAM flags field + bammaskflags: reads BAM and writes BAM while masking (removing) bits + from the flags column + bamrecompress: reads BAM and writes BAM with a defined compression + setting. This tool is capable of multi-threading. + bamsort: reads BAM and writes BAM resorted by coordinates or + query name + bamtofastq: reads BAM and writes FastQ; output can be collated + or uncollated by query name ===================================== debian/copyright ===================================== @@ -0,0 +1,11 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: biobambam2 +Source: https://gitlab.com/german.tischler/biobambam2/tags + +Files: * +Copyright: 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: 2019 Andreas Tille <[email protected]> +License: <license> ===================================== debian/lintian-overrides ===================================== @@ -0,0 +1,2 @@ +# see https://lists.debian.org/debian-med/2018/06/msg00043.html +#PKGNAME#: script-with-language-extension usr/bin/*.* ===================================== debian/rules ===================================== @@ -0,0 +1,31 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 + +include /usr/share/dpkg/default.mk +# this provides: +# DEB_SOURCE: the source package name +# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision) +# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision +# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch +# DEB_VERSION_UPSTREAM: the package's upstream version +# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog +# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as +# specified by <https://reproducible-builds.org/specs/source-date-epoch/> + +# for hardening you might like to uncomment this: +# export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +%: + dh $@ + +### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected +#override_dh_auto_test: +#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) +# do_stuff_for_testing +#endif + +### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script +#get-orig-source: +# . debian/get-orig-source ===================================== debian/source/format ===================================== @@ -0,0 +1 @@ +3.0 (quilt) ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,18 @@ +#!/bin/bash +set -e + +pkg=#PACKAGENAME# + +if [ "${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}" + +#do_stuff_to_test_package# ===================================== debian/upstream/metadata ===================================== @@ -0,0 +1,12 @@ +Reference: + Author: + Title: + Journal: + Year: + Volume: + Number: + Pages: + DOI: + PMID: + URL: + eprint: ===================================== debian/watch ===================================== @@ -0,0 +1,3 @@ +version=4 + +https://gitlab.com/german.tischler/biobambam2/tags?sort=updated_desc .*/archive/.*/biobambam2-@ANY_VERSION@-release-\d+@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/biobambam2/commit/375596d4d4d41095f1985b54a7d1d231c0fd01de -- View it on GitLab: https://salsa.debian.org/med-team/biobambam2/commit/375596d4d4d41095f1985b54a7d1d231c0fd01de You're receiving this email because of your account on salsa.debian.org.
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