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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-cutadapt">Debian Med / q2-cutadapt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac">450edadf</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-06-20T16:15:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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+
debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
<span class="new-file">
+
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="new-file">
+
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
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debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
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debian/rules
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<li class="file-stats">
<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">
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debian/source/format
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
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debian/upstream/metadata
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
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debian/watch
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-cutadapt (2019.4.0-1) 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"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Thu, 20 Jun 2019 17:29:03 +0200</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Source</span><span class="p">:</span> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">cutadapt</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Maintainer</span><span class="p">:</span> <span class="n" style="color: #333;">Debian</span> <span class="n" style="color: #333;">Med</span> <span class="n" style="color: #333;">Packaging</span> <span class="n" style="color: #333;">Team</span> <span class="p"><</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">packaging</span><span class="p">@</span><span class="n" style="color: #333;">lists</span><span class="p">.</span><span class="n" style="color: #333;">alioth</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;">12</span><span class="p">~)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.3.0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">cutadapt</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">cutadapt</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">cutadapt</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">any</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">working</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">adapters</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">data</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"> <span class="n" style="color: #333;">researchers</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">start</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">analysis</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raw</span> <span class="n" style="color: #333;">DNA</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">finish</span> <span class="k" style="font-weight: 600;">with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"> <span class="n" style="color: #333;">publication</span><span class="p">-</span><span class="n" style="color: #333;">quality</span> <span class="n" style="color: #333;">figures</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">statistical</span> <span class="n" style="color: #333;">results</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">Key</span> <span class="n" style="color: #333;">features</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Integrated</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">automatic</span> <span class="n" style="color: #333;">tracking</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">provenance</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Semantic</span> <span class="n" style="color: #333;">type</span> <span class="nf" style="color: #900; font-weight: 600;">system</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Plugin</span> <span class="nf" style="color: #900; font-weight: 600;">system</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">extending</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">functionality</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">types</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">interfaces</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">API</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">graphical</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">redesign</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rewrite</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">address</span> <span class="n" style="color: #333;">many</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limitations</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">retaining</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">features</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">widely</span><span class="p">-</span><span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">supports</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">initial</span> <span class="k" style="font-weight: 600;">end</span><span class="p">-</span><span class="k" style="font-weight: 600;">to</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">functionality</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">regularly</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">through</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugins</span><span class="p">.</span> <span class="n" style="color: #333;">You</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">view</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">availability</span> <span class="n" style="color: #333;">page</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">page</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">being</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">developed</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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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: <pkg></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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<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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<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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<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: 2019 <your_ID></span>
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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-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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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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6
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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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8
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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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9
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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-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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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-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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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-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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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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6
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<pre style="margin: 0;">+<span id="LC6" 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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7
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<pre style="margin: 0;">+<span id="LC7" 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="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="k" style="font-weight: 600;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</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;"># shellcheck disable=SC2064</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" 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-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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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: </span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: </span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: </span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: </span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: </span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: </span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: </span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID:</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: </span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/q2-cutadapt/commit/450edadfc2a67460dc32af0eec363db02e1f00ac#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">https://github.com/qiime2/q2-cutadapt/releases/latest .*/archive/(\d[.\d]+)@ARCHIVE_EXT@</span></pre>
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