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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-diversity">Debian Med / q2-diversity</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/q2-diversity/-/commit/c1dcc5f8b22ea8a569f35344819513d861e853d1">c1dcc5f8</a></strong>
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<span>by Steffen</span>
<i>at 2021-08-12T18:09:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added Nilesh as uploader, improved description and clean
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-diversity/-/commit/c1dcc5f8b22ea8a569f35344819513d861e853d1#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;">diversity</span></span>
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<pre style="margin: 0;"> <span id="LC2" 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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<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">Moeller</span> <span class="p"><</span><span class="n" style="color: #333;">moeller</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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">Moeller</span> <span class="p"><</span><span class="n" style="color: #333;">moeller</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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">Nilesh</span> <span class="n" style="color: #333;">Patra</span> <span class="p"><</span><span class="n" style="color: #333;">nilesh</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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<pre style="margin: 0;"> <span id="LC5" 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="LC6" 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="LC7" 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="n" style="color: #333;">compat</span> <span class="p">(=</span> <span class="m" style="color: #099;">13</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,21 +41,17 @@ Description: QIIME2 plugin for core diversity analysis</td>
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<pre style="margin: 0;"> <span id="LC41" 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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<pre style="margin: 0;"> <span id="LC42" 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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<pre style="margin: 0;"> <span id="LC43" 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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<pre style="margin: 0;">-<span id="LC43" 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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<pre style="margin: 0;">-<span id="LC44" 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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<pre style="margin: 0;">-<span id="LC45" 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="LC46" 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="LC47" 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="LC48" 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="LC49" 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="LC44" 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 class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <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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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="n" style="color: #333;">Functionality</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">made</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>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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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<pre style="margin: 0;">-<span id="LC52" 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="LC53" 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="LC54" 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="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">plugin</span> <span class="n" style="color: #333;">provides</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">means</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">statistically</span> <span class="n" style="color: #333;">assess</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">diversity</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">microbiota</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">direct</span> <span class="n" style="color: #333;">clinical</span> <span class="n" style="color: #333;">interest</span><span class="p">,</span> <span class="n" style="color: #333;">since</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">whatever</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">eat</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">antibiotics</span> <span class="n" style="color: #333;">applied</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">survival</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">different</span> <span class="n" style="color: #333;">groups</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">bacteria</span><span class="p">/</span><span class="n" style="color: #333;">yeasts</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">affected</span><span class="p">.</span> <span class="k" style="font-weight: 600;">From</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">relative</span> <span class="n" style="color: #333;">abundances</span> <span class="k" style="font-weight: 600;">of</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">strains</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">constribute</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">microbiome</span><span class="p">,</span> <span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">prominently</span><span class="p">,</span> <span class="n" style="color: #333;">comparisons</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">within</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">group</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">samples</span> <span class="p">(</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">individual</span><span class="p">)</span> <span class="n" style="color: #333;">determines</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">alpha</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">diversity</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">between</span> <span class="p">(</span><span class="n" style="color: #333;">groups</span> <span class="k" style="font-weight: 600;">of</span><span class="p">)</span> <span class="n" style="color: #333;">samples</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">beta</span> <span class="n" style="color: #333;">diversity</span> <span class="n" style="color: #333;">is</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="n" style="color: #333;">inspected</span><span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC56" 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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<pre style="margin: 0;">-<span id="LC57" 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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<pre style="margin: 0;">-<span id="LC58" 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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<pre style="margin: 0;">-<span id="LC59" 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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<pre style="margin: 0;">-<span id="LC60" class="line" lang="mosel"> <span class="n" style="color: #333;">developed</span><span class="p">.</span></span></pre>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">key</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">most</span> <span class="n" style="color: #333;">workflows</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qiime</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-diversity/-/commit/c1dcc5f8b22ea8a569f35344819513d861e853d1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,3 +33,4 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> rm -rf q2_diversity.egg-info</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> find q2_diversity -name node_modules -type d | xargs -r rm -rf</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> find q2_diversity/_alpha -name dist -type d | xargs -r rm -rf</span></pre>
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