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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/swarm-cluster">Debian Med / swarm-cluster</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/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de">b4a8c15a</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-06-16T19:14:47+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
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<h4>8 changed files:</h4>
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debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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debian/source/include-binaries
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debian/tests/control
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debian/tests/run-unit-test
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debian/tests/test-data/input.fasta.gz
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#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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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="php"><span class="nx">_______________________________________</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 noteable_line" 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">execution</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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<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 id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">swarm-cluster (2.2.2+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add autopkgtest</span>
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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"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Sat, 16 Jun 2018 19:08:01 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">swarm-cluster (2.2.2+dfsg-1) unstable; urgency=medium</span>
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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"> * New upstream version (no pdf versions of makefiles any more)</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="696" 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="696" 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">@@ -696,3 +696,21 @@ Copyright: 2014-2015 Tim Booth <tbooth@ceh.ac.uk></td>
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="plaintext">License: GPL-3+</span>
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697
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="plaintext"> On Debian Systems you can find a copy of the GNU GENERAL PUBLIC LICENSE</span>
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698
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="plaintext"> at /usr/share/common-licenses/GPL-3.</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext"></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext">Files: debian/tests/test-data/input.fasta.gz</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext">Copyright: 1996-2018 NCBI</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext">License: unrestricted</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext"> Databases of molecular data on the NCBI Web site include such examples as</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext"> nucleotide sequences (GenBank), protein sequences, macromolecular structures,</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext"> molecular variation, gene expression, and mapping data. They are designed to</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext"> provide and encourage access within the scientific community to sources of</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext"> current and comprehensive information. Therefore, NCBI itself places no</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext"> restrictions on the use or distribution of the data contained therein. Nor do</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext"> we accept data when the submitter has requested restrictions on reuse or</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext"> redistribution.</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext">Comment:</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext"> The test data file was prepared from a SRA data file with accession number</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext"> SRR7082946 according to the instructions described in README.html</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext"> .</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext"> To download the original file you can use fastq-dump tool from SRA Toolkit:</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext"> fastq-dump SRR7082946</span></pre>
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<a href="https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.html</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/test-data</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/README.test</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/test-data/input.fasta.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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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/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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/sh -e</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"swarm"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test-data/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</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;">gunzip</span> <span class="k" style="font-weight: 600;">*</span>.gz</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing swarm with parameters recommended...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">swarm <span class="nt" style="color: navy;">-f</span> <span class="nt" style="color: navy;">-w</span> OTUs.fasta input.fasta <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> OTUs.fasta <span class="o" style="font-weight: 600;">]</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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">PASS"</span></span></pre>
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