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<h3>
Aikaterini Kalou pushed to branch master
at <a href="https://salsa.debian.org/med-team/rsem">Debian Med / rsem</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3">18c02c28</a></strong>
<div>
<span>by Aikaterini Kalou</span>
<i>at 2018-03-14T19:20:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added autopkgtest
</pre>
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<h4>8 changed files:</h4>
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<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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+
debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#9276f3a59769ef229d82dbcea3cbc85db0c15282">
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debian/examples/mouse_ref_building_from_transcripts.tar.gz
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<li class="file-stats">
<a href="#921bc987ca017a5a778efff41c2e1dfe831baeed">
debian/rsem.docs
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<li class="file-stats">
<a href="#84e56b38ae633116f3050b45cbea71ca64a6945f">
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debian/rsem.examples
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
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debian/source/include-binaries
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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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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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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">
4
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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">executing</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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6
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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>
</pre>
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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="php"></span>
</pre>
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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="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>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="nx">Note</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">The</span> <span class="nx">sample</span> <span class="nx">data</span> <span class="nx">are</span> <span class="nx">obtained</span> <span class="nx">via</span></span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"> <span class="nx">wget</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">q</span> <span class="nx">https</span><span class="o" style="font-weight: 600;">://</span><span class="nx">www</span><span class="o" style="font-weight: 600;">.</span><span class="nx">dropbox</span><span class="o" style="font-weight: 600;">.</span><span class="nx">com</span><span class="o" style="font-weight: 600;">/</span><span class="nx">s</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ie67okalzaw8zzj</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mouse_ref_building_from_transcripts</span><span class="o" style="font-weight: 600;">.</span><span class="nx">tar</span><span class="o" style="font-weight: 600;">.</span><span class="nx">gz</span><span class="o" style="font-weight: 600;">?</span><span class="nb" style="color: #0086b3;">dl</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">O</span> <span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mouse_ref_building_from_transcripts</span><span class="o" style="font-weight: 600;">.</span><span class="nx">tar</span><span class="o" style="font-weight: 600;">.</span><span class="nx">gz</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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="php"><span class="nx">More</span> <span class="nx">examples</span> <span class="k" style="font-weight: 600;">and</span> <span class="nx">datasets</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">found</span> <span class="nx">at</span> <span class="nx">https</span><span class="o" style="font-weight: 600;">://</span><span class="nx">github</span><span class="o" style="font-weight: 600;">.</span><span class="nx">com</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bli25ucb</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RSEM_tutorial</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">rsem (1.3.0+dfsg-1) experimental; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rsem (1.3.0+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="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"> -- Katerina Kalou <aik.kalou@gmail.com> Wed, 14 Mar 2018 18:32:55 +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">rsem (1.3.0+dfsg-1) UNRELEASED; 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</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * d/watch:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> - version=4</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> - xz compression</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * remove code copy of samtools-1.3</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> * d/rules: do not parse d/changelog</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sun, 18 Feb 2018 20:34:37</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 09 Dec 2016 14:26:08</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">rsem (1.2.31+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">WHAT_IS_NEW</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">cnt_file_description.txt</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">model_file_description.txt</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#84e56b38ae633116f3050b45cbea71ca64a6945f"><strong>debian/rsem.examples</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/examples/*</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mouse_ref_building_from_transcripts.tar.gz</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#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>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3#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: navy;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</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="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"rsem"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></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="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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>mktemp <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="sb" style="color: #d14;">`</span></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;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell">cp <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-C</span> <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-xzf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</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="shell"></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="shell">rsem-prepare-reference <span class="se" style="color: #d14;">\</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nt" style="color: navy;">--transcript-to-gene-map</span> mouse_ref_mapping.txt <span class="se" style="color: #d14;">\</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> mouse_ref.fa mouse_ref</span></pre>
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