[med-svn] [Git][med-team/biobambam2][master] Initial packaging
Andreas Tille
gitlab at salsa.debian.org
Fri Apr 12 10:18:40 BST 2019
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <tille at debian.org>
+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- at ANY_VERSION@-release-\d+ at 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
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