[med-svn] [Git][med-team/q2-feature-classifier][master] Initial packaging
Liubov Chuprikova
gitlab at salsa.debian.org
Thu Jul 4 09:27:53 BST 2019
Liubov Chuprikova pushed to branch master at Debian Med / q2-feature-classifier
Commits:
9406b379 by Liubov Chuprikova at 2019-07-04T08:23:17Z
Initial packaging
- - - - -
11 changed files:
- + debian/README.test
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + 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 +1,5 @@
+q2-feature-classifier (2019.4.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com> Wed, 03 Jul 2019 19:59:31 +0200
=====================================
debian/compat
=====================================
@@ -0,0 +1 @@
+12
=====================================
debian/control
=====================================
@@ -0,0 +1,37 @@
+Source: q2-feature-classifier
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>
+Build-Depends: debhelper (>= 12~)
+Standards-Version: 4.3.0
+Vcs-Browser: https://salsa.debian.org/med-team/q2-feature-classifier
+Vcs-Git: https://salsa.debian.org/med-team/q2-feature-classifier.git
+Homepage: https://qiime2.org/
+
+Package: q2-feature-classifier
+Architecture: all
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: QIIME 2 plugin supporting taxonomic classification
+ QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
+ package with a focus on data and analysis transparency. QIIME 2 enables
+ researchers to start an analysis with raw DNA sequence data and finish with
+ publication-quality figures and statistical results.
+ Key features:
+ * Integrated and automatic tracking of data provenance
+ * Semantic type system
+ * Plugin system for extending microbiome analysis functionality
+ * Support for multiple types of user interfaces (e.g. API, command line,
+ graphical)
+ .
+ QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
+ pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
+ retaining the features that makes QIIME 1 a powerful and widely-used analysis
+ pipeline.
+ .
+ QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
+ New functionality will regularly become available through QIIME 2 plugins. You
+ can view a list of plugins that are currently available on the QIIME 2 plugin
+ availability page. The future plugins page lists plugins that are being
+ developed.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,58 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: QIIME 2
+Source: https://github.com/qiime2/q2-feature-classifier/releases
+
+Files: *
+Copyright: 2016-2019 QIIME 2 development team
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2019 Liubov Chuprikova <chuprikovalv at gmail.com>
+ Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ 3. Neither the name of the copyright holder nor the names of its
+ contributors may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ For other licensing arrangements, please contact Daniel J. Schaid.
+ .
+ On a Debian system, the GNU GPL license version 2 is distributed in the
+ file /usr/share/common-licenses/GPL-2.
=====================================
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 +1,40 @@
+Reference:
+ Author: >
+ Evan Bolyen and Jai Ram Rideout and Matthew R Dillon and Nicholas A
+ Bokulich and Christian Abnet and Gabriel A Al-Ghalith and Harriet Alexander and
+ Eric J Alm and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and
+ Jordan E Bisanz and Kyle Bittinger and Asker Brejnrod and Colin J Brislawn and
+ C Titus Brown and Benjamin J Callahan and Andrés Mauricio Caraballo-Rodríguez
+ and John Chase and Emily Cope and Ricardo Da Silva and Pieter C Dorrestein and
+ Gavin M Douglas and Daniel M Durall and Claire Duvallet and Christian F
+ Edwardson and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and
+ Julia M Gauglitz and Deanna L Gibson and Antonio Gonzalez and Kestrel Gorlick
+ and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and
+ Curtis Huttenhower and Gavin Huttley and Stefan Janssen and Alan K Jarmusch and
+ Lingjing Jiang and Benjamin Kaehler and Kyo Bin Kang and Christopher R Keefe
+ and Paul Keim and Scott T Kelley and Dan Knights and Irina Koester and Tomasz
+ Kosciolek and Jorden Kreps and Morgan GI Langille and Joslynn Lee and Ruth Ley
+ and Yong-Xin Liu and Erikka Loftfield and Catherine Lozupone and Massoud Maher
+ and Clarisse Marotz and Bryan D Martin and Daniel McDonald and Lauren J McIver
+ and Alexey V Melnik and Jessica L Metcalf and Sydney C Morgan and Jamie Morton
+ and Ahmad Turan Naimey and Jose A Navas-Molina and Louis Felix Nothias and
+ Stephanie B Orchanian and Talima Pearson and Samuel L Peoples and Daniel Petras
+ and Mary Lai Preuss and Elmar Pruesse and Lasse Buur Rasmussen and Adam Rivers
+ and Michael S Robeson and Patrick Rosenthal and Nicola Segata and Michael
+ Shaffer and Arron Shiffer and Rashmi Sinha and Se Jin Song and John R Spear and
+ Austin D Swafford and Luke R Thompson and Pedro J Torres and Pauline Trinh and
+ Anupriya Tripathi and Peter J Turnbaugh and Sabah Ul-Hasan and Justin JJ van
+ der Hooft and Fernando Vargas and Yoshiki Vázquez-Baeza and Emily Vogtmann and
+ Max von Hippel and William Walters and Yunhu Wan and Mingxun Wang and Jonathan
+ Warren and Kyle C Weber and Chase HD Williamson and Amy D Willis and Zhenjiang
+ Zech Xu and Jesse R Zaneveld and Yilong Zhang and Qiyun Zhu and Rob Knight and
+ J Gregory Caporaso
+ Title: >
+ QIIME 2: Reproducible, interactive, scalable, and extensible microbiome
+ data science
+ Journal: PeerJ Preprints
+ Year: 2018
+ Volume: 6
+ DOI: 10.7287/peerj.preprints.27295v2
+ URL: https://peerj.com/preprints/27295/
+ eprint: https://peerj.com/preprints/27295.pdf
=====================================
debian/watch
=====================================
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/qiime2/q2-feature-classifier/releases/latest .*/archive/(\d[.\d]+)@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/q2-feature-classifier/commit/9406b379425e8043e9370016c322af5c8b80e08b
--
View it on GitLab: https://salsa.debian.org/med-team/q2-feature-classifier/commit/9406b379425e8043e9370016c322af5c8b80e08b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190704/e86e599e/attachment-0001.html>
More information about the debian-med-commit
mailing list