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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/nanook">Debian Med / nanook</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanook/-/commit/54ed425dbf6594ee30db0a14e20431574cf508d7">54ed425d</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-28T04:53:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add test and reference data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanook/-/commit/59b3abc625466c478ddc9e865be144aef5e25f99">59b3abc6</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-28T04:53:25+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/nanook/-/commit/a76719c53704128eb1d149d16c857844a5be8490">a76719c5</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-06-28T04:53:57+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
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<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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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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">
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debian/examples
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<a href="#a2a565aa25c2bf10949e3702636a59d9f1110a11">
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debian/tests/README.test_data
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debian/tests/control
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<a href="#ddc8c201d0a2beefe0e95d241f2244d9f870ff7e">
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debian/tests/data.tar.gz
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debian/tests/ref.tar.gz
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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/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#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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<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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<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="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">nanook (1.33+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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Hervé Ménager ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * correct bio.tools and scicrunch refs</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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/u/metadata: yamllint</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Add test and reference data</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sun, 28 Jun 2020 04:53:32 +0530</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">nanook (1.33+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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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*</span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/README*</span></pre>
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<a href="https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/*</span></pre>
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<a href="https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#a2a565aa25c2bf10949e3702636a59d9f1110a11"><strong>debian/tests/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">data.tar.gz is a subset of the data available at </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">https://opendata.earlham.ac.uk/opendata/nanook/nanook_ecoli_500.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ref.tar.gz contains results obtained by processing this data as described at</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">https://nanook.readthedocs.io/en/latest/tutorial.html</span></pre>
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<a href="https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490#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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>nanook</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xf data.tar.gz</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>xf ref.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>data/nanook_ecoli_500/references</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">lastdb <span class="nt" style="color: #000080;">-Q</span> 0 ecoli_dh10b_cs ecoli_dh10b_cs.fasta</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">nanook extract <span class="nt" style="color: #000080;">-s</span> N79596_dh10b_8kb_11022015</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">nanook align <span class="nt" style="color: #000080;">-s</span> N79596_dh10b_8kb_11022015 <span class="nt" style="color: #000080;">-r</span> references/ecoli_dh10b_cs.fasta</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">nanook analyse <span class="nt" style="color: #000080;">-s</span> N79596_dh10b_8kb_11022015 <span class="nt" style="color: #000080;">-r</span> references/ecoli_dh10b_cs.fasta <span class="nt" style="color: #000080;">-passonly</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../..</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>file <span class="k" style="font-weight: 600;">in </span>ref/<span class="k" style="font-weight: 600;">*</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$file</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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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">=</span>data<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="p">#ref</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> diff <span class="nv" style="color: #008080;">$file</span> <span class="nv" style="color: #008080;">$output</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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