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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-vsearch">Debian Med / q2-vsearch</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944">4d562c48</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-05T20:26:01+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<h4>10 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
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debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
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debian/copyright
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debian/rules
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<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
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debian/salsa-ci.yml
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debian/source/format
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debian/tests/control
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debian/tests/run-unit-test
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debian/upstream/metadata
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debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-vsearch (2020.8.0.dev0-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Shayan Doust <hello@shayandoust.me> Sun, 05 Jul 2020 19:57:45 +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: q2-vsearch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/q2-vsearch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/q2-vsearch.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/qiime2/q2-vsearch</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Package: q2-vsearch</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Description: QIIME 2 plugin for clustering and dereplicating with vsearch</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Wraps the vsearch application, and provides methods for clustering and</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dereplicating features and sequences.</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: q2-vsearch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: <path_to_download></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Comment: **** Before manually editing this file you should give ****</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> scan-copyrights</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> **** available in cme + lib-config-model-dpkg-perl ****</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> **** package a try. For existing copyright files try ****</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> cme update dpkg-copyright</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Files: *</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Copyright: 20xx-20yy <upstream></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: <license></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Files: debian/*</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Copyright: 2020 Shayan Doust <hello@shayandoust.me></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: <license></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;">#PACKAGENAME#</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince & Frédéric Mahé</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: "VSEARCH: a versatile open source tool for metagenomics"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: PeerJ</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2016</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 4</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> DOI: 10.7717/peerj.2584</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> URL: https://peerj.com/articles/2584/</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Other-Reference: https://raw.githubusercontent.com/qiime2/q2-vsearch/master/q2_vsearch/citations.bib</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">https://github.com/qiime2/q2-vsearch/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>
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