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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/jaligner">Debian Med / jaligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jaligner/-/commit/36fe8b76356f6d23cde217fac4d8e3f3b54f0651">36fe8b76</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:12:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install example and reference data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jaligner/-/commit/a1f25fdf602258cfe90f626fe4db7f0678246f3b">a1f25fdf</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:16:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jaligner/-/commit/4cce27a5da89b8f6e312674c18bbc868a015e3c3">4cce27a5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:16:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jaligner/-/commit/ead4e86414174e44e6bb3d63be975f4cf315adb7">ead4e864</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:17:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Pranav Ballaney to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jaligner/-/commit/01a98951682a3f5f013daa2a8723b74f89b1cb45">01a98951</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:19:54+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include reference binary
</pre>
</li>
</ul>
<h4>9 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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
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+
debian/docs
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
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<li class="file-stats">
<a href="#a2a565aa25c2bf10949e3702636a59d9f1110a11">
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+
debian/tests/README.test_data
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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="#ae8ea6302b042802d9442fa6f83b198759959c87">
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debian/tests/references.tar.xz
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
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debian/tests/run-unit-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#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="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="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="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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<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="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: jaligner</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</span>
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Michael R. Crusoe <michael.crusoe@gmail.com>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/README*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">src/jaligner/example/sequences/*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/reference*</span></pre>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</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">@@ -7,3 +7,4 @@ debian/images/open.gif</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">debian/images/paste.gif</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">debian/images/print.gif</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">debian/images/save.gif</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">debian/tests/references.tar.xz</span></pre>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#a2a565aa25c2bf10949e3702636a59d9f1110a11"><strong>debian/tests/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">references.tar.xz contains output files produced by running jaligner on </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">p53_human and p53_mouse, which come with the jaligner package. </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">The jaligner command is provided in run-unit-test.</span></pre>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#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/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#ae8ea6302b042802d9442fa6f83b198759959c87"><strong>debian/tests/references.tar.xz</strong></a>
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<a href="https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45#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/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>jaligner</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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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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;">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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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;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xf</span> references.tar.xz</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-R</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">matrices</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> /usr/share/jaligner/jaligner/matrix/matrices<span class="si" style="color: #d14;">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>matrix <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$matrices</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>jaligner p53_human.fasta p53_mouse.fasta <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">matrix</span><span class="k" style="font-weight: 600;">}</span> 10 0.5 <span class="o" style="font-weight: 600;">></span> result.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">matrix</span><span class="k" style="font-weight: 600;">}</span>.txt</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> diff reference.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">matrix</span><span class="k" style="font-weight: 600;">}</span>.txt result.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">matrix</span><span class="k" style="font-weight: 600;">}</span>.txt</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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