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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/gasic">Debian Med / gasic</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/a1b7dda5a88a3b161b7e0a02fbee9346d9fbbd9e">a1b7dda5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-09T04:36:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest template
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/a54f060ccc6619a13476079d755ab6d4d8996529">a54f060c</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-10T02:50:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/507482db6ceb08f765d58a5a57b702894d8dfe0f">507482db</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-10T02:50:28+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/gasic/-/commit/d72532ed7b70713f43233bc7b2087b6b622507b5">d72532ed</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-10T02:53:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs and update changelog
</pre>
</li>
</ul>
<h4>18 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">
debian/docs
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<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
debian/examples
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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debian/tests/data/README.test_data
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debian/tests/data/genomes/dwv.fasta-e.gz
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debian/tests/data/genomes/dwv.fasta.fai.gz
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debian/tests/data/genomes/dwv.fasta.gz
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debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz
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debian/tests/data/names.gz
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debian/tests/data/reads/SRR059298_subset.fastq.gz
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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/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#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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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">
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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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<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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7
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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/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gasic (0.0.r19-6) 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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/u/metadata: fixed yaml</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"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Install examples</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sun, 10 May 2020 02:52:45 +0530</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">gasic (0.0.r19-5) unstable; urgency=medium</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"> * Use 2to3 to port to Python3</span>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">doc/MANUAL</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/data/README.test_data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">doc/example_script.py</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/README.example</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#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/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#9400395398704fe42840ce7005f56d88482d8867"><strong>debian/tests/data/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Files: genomes/*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Source: https://github.com/seqan/knime_seqan_workflows/blob/master/metagenomics_gasic_workflow/bee_example.zip</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">Files: reads/*</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Source: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR059298</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">The file SRR059298_subset.fastq contains the first 400000 lines </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">from the fastq file obtained from the above source.</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">Files: names</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">This was written by Pranav Ballaney <ballaneypranav@gmail.com> for the tests.</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#d05d19370642bb823275fab19a195aeecd6e5147"><strong>debian/tests/data/genomes/dwv.fasta-e.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#5d4cae908ab9d5521dde0c511d816917868811f9"><strong>debian/tests/data/genomes/dwv.fasta.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#bcb71e30c602e39499e35e155133da229c12f742"><strong>debian/tests/data/genomes/vdv1.fasta.fai.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5#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: #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>gasic</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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<td class="diff-line-num new new_line" data-linenumber="15" 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">
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>
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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;">cd </span>genomes</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">bowtie-build dwv.fasta dwv.fasta</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">bowtie-build vdv1.fasta vdv1.fasta </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">run_mappers names reads/SRR059298_subset.fastq <span class="nt" style="color: #000080;">-i</span> ./genomes/%s.fasta <span class="nt" style="color: #000080;">-o</span> ./SAM/mapped_%s.sam <span class="nt" style="color: #000080;">-m</span> bowtie</span></pre>
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