[med-svn] [Git][med-team/seqkit][master] Initial packaging attempt
Andreas Tille
gitlab at salsa.debian.org
Sat Jun 27 09:29:02 BST 2020
Andreas Tille pushed to branch master at Debian Med / seqkit
Commits:
153df7cd by Andreas Tille at 2020-06-27T10:28:50+02:00
Initial packaging attempt
- - - - -
8 changed files:
- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+seqkit (0.12.1-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 27 Jun 2020 08:34:29 +0200
=====================================
debian/control
=====================================
@@ -0,0 +1,25 @@
+Source: seqkit
+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-compat (= 13),
+ dh-golang,
+ golang-any
+Standards-Version: 4.5.0
+Vcs-Browser: https://salsa.debian.org/med-team/seqkit
+Vcs-Git: https://salsa.debian.org/med-team/seqkit.git
+Homepage: https://github.com/shenwei356/seqkit
+
+Package: seqkit
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: cross-platform and ultrafast toolkit for FASTA/Q file manipulation
+ SeqKit describes a cross-platform ultrafast comprehensive toolkit for
+ FASTA/Q processing. SeqKit provides executable binary files for all
+ major operating systems, including Windows, Linux, and Mac OS X, and can
+ be directly used without any dependencies or pre-configurations. SeqKit
+ demonstrates competitive performance in execution time and memory usage
+ compared to similar tools. The efficiency and usability of SeqKit enable
+ researchers to rapidly accomplish common FASTA/Q file manipulations.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,30 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SeqKit
+Source: https://github.com/shenwei356/seqkit/releases
+
+Files: *
+Copyright: 2016-2020 Wei Shen, 2019 Oxford Nanopore Technologies.
+License: MIT
+
+Files: debian/*
+Copyright: 2020 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
=====================================
debian/rules
=====================================
@@ -0,0 +1,27 @@
+#!/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 $@ --buildsystem=golang --with=golang --builddirectory=build # --sourcedirectory=seqkit
+
+### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
+#override_dh_auto_test:
+#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+# do_stuff_for_testing
+#endif
=====================================
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/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,17 @@
+Reference:
+ Author: Wei Shen and Shuai Le and Yan Li and Fuquan Hu
+ Title: >
+ SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
+ Journal: PlosOne
+ Year: 2016
+ Volume: 11
+ Number: 10
+ Pages: e0163962
+ DOI: 10.1371/journal.pone.0163962
+ PMID: 27706213
+ PMCID: PMC5051824
+ URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163962
+ eprint: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0163962&type=printable
+Registry:
+ - Name: conda:bioconda
+ Entry: seqkit
=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+https://github.com/shenwei356/seqkit/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/153df7cd071cdcdcf2f848d0c6765e197159cc9a
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/153df7cd071cdcdcf2f848d0c6765e197159cc9a
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